diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib
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@@ -1,4654 +0,0 @@
-@phdthesis{___2019,
- author = {{Евгений Игоревич}},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- school = {РОССИЙСКАЯ АКАДЕМИЯ НАУК ИНСТИТУТ ЦИТОЛОГИИ},
- title = {{РОЛЬ} БЕЛКОВ {HNRNP}-{KИ} {PCBP1} В ПЛЮРИПОТЕНТНЫХ СТВОЛОВЫХ КЛЕТКАХМЫШИ},
- url = {https://www.incras.ru/wp-content/uploads/2019/10/polnyj-tekst-dissertacii_bahmet_e_i2.pdf},
- year = {2019}
-}
-
-@article{afouda_culturing_2020,
- abstract = {Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23\% to 55.59\%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.},
- author = {Afouda, Pamela and Dubourg, Grégory and Levasseur, Anthony and Fournier, Pierre-Edouard and Delerce, Jeremy and Mediannikov, Oleg and Diene, Seydina M. and Nahon, Daniel and Bourlès, Didier and Rolain, Jean-Marc and Raoult, Didier},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/microorganisms8101522},
- journal = {Microorganisms},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Siberian permafrost, culturomics, genomic evolution, resistance genes},
- language = {en},
- month = {October},
- note = {Number: 10
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {10},
- pages = {1522},
- title = {Culturing {Ancient} {Bacteria} {Carrying} {Resistance} {Genes} from {Permafrost} and {Comparative} {Genomics} with {Modern} {Isolates}},
- url = {https://www.mdpi.com/2076-2607/8/10/1522},
- urldate = {2021-01-15},
- volume = {8},
- year = {2020}
-}
-
-@article{aggarwal_role_2021,
- author = {Aggarwal, Dinesh and Myers, Richard and Hamilton, William L. and Bharucha, Tehmina and Tumelty, Niamh M. and Brown, Colin S. and Meader, Emma J. and Connor, Tom and Smith, Darren L. and Bradley, Declan T. and Robson, Samuel and Bashton, Matthew and Shallcross, Laura and Zambon, Maria and Goodfellow, Ian and Chand, Meera and O'Grady, Justin and Török, M. Estée and Peacock, Sharon J. and Page, Andrew J.},
- doi = {10.1016/s2666-5247(21)00208-1},
- journal = {The Lancet Microbe},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Elsevier BV},
- title = {The role of viral genomics in understanding {COVID}-19 outbreaks in long-term care facilities},
- url = {https://doi.org/10.1016/s2666-5247(21)00208-1},
- year = {2021}
-}
-
-@article{ahmad_development_2019,
- abstract = {Premise Alkanna tinctoria (Boraginaceae) is an important medicinal herb with its main distribution across the Mediterranean region. To reveal its genetic variation and population structure, microsatellite markers were developed and validated in four Greek populations. Methods and Results RNA-Seq data of the related species Arnebia euchroma and Echium plantagineum were assembled and mined to identify conserved ortholog sets containing simple sequence repeat motifs. Fifty potential loci were identified and then tested on A. tinctoria, of which 17 loci were polymorphic. The number of alleles ranged from one to nine, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.820, respectively. Most of these loci could be successfully amplified in eight other species of Boraginaceae (Alkanna graeca, A. hellenica, A. sfikasiana, Echium vulgare, E. plantagineum, Lithospermum officinale, Borago officinalis, and Anchusa officinalis). Conclusions This study provides the first set of microsatellite loci for studying the genetic variation and population structure of A. tinctoria and shows their potential usefulness in other Boraginaceae species.},
- author = {Ahmad, Muhammad and Lazic, Desanka and Hansel‐Hohl, Karin and Lexer, Christian and Sehr, Eva Maria},
- doi = {10.1002/aps3.11296},
- issn = {2168-0450},
- journal = {Applications in Plant Sciences},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Alkanna tinctoria, Boraginaceae, conserved ortholog set, microsatellites, population structure},
- language = {en},
- number = {10},
- pages = {e11296},
- title = {Development of novel microsatellite markers for {Alkanna} tinctoria by comparative transcriptomics},
- url = {https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11296},
- urldate = {2019-11-26},
- volume = {7},
- year = {2019}
-}
-
-@article{ahmed_high_2020,
- abstract = {Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95\% CI 0.96–3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion.},
- author = {Ahmed, Shahana and Das, Tridip and Islam, Md Zohorul and Herrero-Fresno, Ana and Biswas, Paritosh Kumar and Olsen, John Elmerdahl},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-75608-2},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {18637},
- title = {High prevalence of mcr-1 -encoded colistin resistance in commensal {Escherichia} coli from broiler chicken in {Bangladesh}},
- url = {https://www.nature.com/articles/s41598-020-75608-2},
- urldate = {2021-02-25},
- volume = {10},
- year = {2020}
-}
-
-@article{alcaraz_development_2021,
- abstract = {There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01\% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.},
- author = {Alcaraz, Alper James G. and Potěšil, David and Mikulášek, Kamil and Green, Derek and Park, Bradley and Burbridge, Connor and Bluhm, Kerstin and Soufan, Othman and Lane, Taylor and Pipal, Marek and Brinkmann, Markus and Xia, Jianguo and Zdráhal, Zbyněk and Schneider, David and Crump, Doug and Basu, Niladri and Hogan, Natacha and Hecker, Markus},
- doi = {10.1021/acs.est.0c05942},
- issn = {0013-936X},
- journal = {Environmental Science \& Technology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: American Chemical Society},
- number = {8},
- pages = {5024--5036},
- title = {Development of a {Comprehensive} {Toxicity} {Pathway} {Model} for 17α-{Ethinylestradiol} in {Early} {Life} {Stage} {Fathead} {Minnows} ({Pimephales} promelas)},
- url = {https://doi.org/10.1021/acs.est.0c05942},
- urldate = {2021-08-20},
- volume = {55},
- year = {2021}
-}
-
-@article{ali_characterization_2021,
- author = {Ali, Renee and Jayaraman, Jayaraj and Mohammed, Azad and Chinnaraja, Chinnadurai and Carrington, Christine V. F. and Severson, David W. and Ramsubhag, Adesh},
- doi = {10.21203/rs.3.rs-380784/v1},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Research Square Platform LLC},
- title = {Characterization of the {Virome} {Associated} {With} {Haemagogus} {Mosquitoes} in {Trinidad}, {West} {Indies}},
- url = {https://doi.org/10.21203/rs.3.rs-380784/v1},
- year = {2021}
-}
-
-@article{amaral_tcti_2022,
- author = {Amaral, Milena do and Freitas, Ana Camila Oliveira and Santos, Ariana Silva and Santos, Everton Cruz dos and Ferreira, Monaliza Macêdo and Gesteira, Abelmon da Silva and Gramacho, Karina Peres and Marinho-Prado, Jeanne Scardini and Pirovani, Carlos Priminho},
- doi = {10.1038/s41598-021-04700-y},
- journal = {Scientific Reports},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {{TcTI}, a {Kunitz}-type trypsin inhibitor from cocoa associated with defense against pathogens},
- url = {https://doi.org/10.1038/s41598-021-04700-y},
- volume = {12},
- year = {2022}
-}
-
-@article{apostolakos_occurrence_2021,
- author = {Apostolakos, Ilias and Laconi, Andrea and Mughini-Gras, Lapo and Yapicier, Özlem Şahan and Piccirillo, Alessandra},
- doi = {10.3389/fvets.2021.737720},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Frontiers Media SA},
- title = {Occurrence of {Colibacillosis} in {Broilers} and {Its} {Relationship} {With} {Avian} {Pathogenic} {Escherichia} coli ({APEC}) {Population} {Structure} and {Molecular} {Characteristics}},
- url = {https://doi.org/10.3389/fvets.2021.737720},
- volume = {8},
- year = {2021}
-}
-
-@article{arcari_interplay_2022,
- author = {Arcari, Gabriele and Oliva, Alessandra and Sacco, Federica and Lella, Federica Maria Di and Raponi, Giammarco and Tomolillo, Dario and Curtolo, Ambrogio and Venditti, Mario and Carattoli, Alessandra},
- doi = {10.1007/s10096-021-04388-y},
- journal = {European Journal of Clinical Microbiology \& Infectious Diseases},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {3},
- pages = {495--500},
- title = {Interplay between {Klebsiella} pneumoniae producing {KPC}-31 and {KPC}-3 under treatment with high dosage meropenem: a case report},
- url = {https://doi.org/10.1007/s10096-021-04388-y},
- volume = {41},
- year = {2022}
-}
-
-@incollection{bagnacani_tools_2019,
- abstract = {MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. The use of RNA data in gene expression analysis has become increasingly important to gain insights into the regulatory mechanisms behind miRNA–mRNA interactions. As a result, we are confronted with a growing landscape of tools, while standards for reproducibility and benchmarking lag behind. This work identifies the challenges for reproducible RNA analysis, and highlights best practices on the processing and dissemination of scientific results. We found that the success of a tool does not solely depend on its performances: equally important is how a tool is received, and then supported within a community. This leads us to a detailed presentation of the RNA workbench, a community effort for sharing workflows and processing tools, built on top of the Galaxy framework. Here, we follow the community guidelines to extend its portfolio of RNA tools with the integration of the TriplexRNA (https://triplexrna.org). Our findings provide the basis for the development of a recommendation system, to guide users in the choice of tools and workflows.},
- address = {New York, NY},
- author = {Bagnacani, Andrea and Wolfien, Markus and Wolkenhauer, Olaf},
- booktitle = {Computational {Biology} of {Non}-{Coding} {RNA}: {Methods} and {Protocols}},
- doi = {10.1007/978-1-4939-8982-9_8},
- editor = {Lai, Xin and Gupta, Shailendra K. and Vera, Julio},
- isbn = {978-1-4939-8982-9},
- keywords = {+Galactic, +HowTo, +RefPublic, +Reproducibility, +Tools, {\textgreater}RNA Workbench, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Database, Galaxy, Gene regulation, RNA workbench, miRNA–mRNA interactions},
- language = {en},
- pages = {199--214},
- publisher = {Springer New York},
- series = {Methods in {Molecular} {Biology}},
- title = {Tools for {Understanding} {miRNA}–{mRNA} {Interactions} for {Reproducible} {RNA} {Analysis}},
- url = {https://doi.org/10.1007/978-1-4939-8982-9_8},
- urldate = {2019-01-25},
- year = {2019}
-}
-
-@article{baker_no_2020,
- abstract = {The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.},
- author = {Baker, Dannon and Beek, Marius van den and Blankenberg, Daniel and Bouvier, Dave and Chilton, John and Coraor, Nate and Coppens, Frederik and Eguinoa, Ignacio and Gladman, Simon and Grüning, Björn and Keener, Nicholas and Larivière, Delphine and Lonie, Andrew and Pond, Sergei Kosakovsky and Maier, Wolfgang and Nekrutenko, Anton and Taylor, James and Weaver, Steven},
- doi = {10.1371/journal.ppat.1008643},
- issn = {1553-7374},
- journal = {PLOS Pathogens},
- keywords = {+Galactic, +IsGalaxy, +Methods, +Project, +Reproducibility, +Shared, +UseMain, +UsePublic, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, COVID 19, Genome analysis, Genomics, Open source software, Preprocessing, SARS, SARS CoV 2, Transmissible gastroenteritis coronavirus},
- language = {en},
- month = {August},
- note = {Publisher: Public Library of Science},
- number = {8},
- pages = {e1008643},
- shorttitle = {No more business as usual},
- title = {No more business as usual: {Agile} and effective responses to emerging pathogen threats require open data and open analytics},
- url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008643},
- urldate = {2020-08-30},
- volume = {16},
- year = {2020}
-}
-
-@phdthesis{baldwin_evaluating_2019,
- abstract = {Chlorpyrifos (CPF) is an organophosphate pesticide used extensively in Canada and around the world. Due to its highly conserved mechanism of action involving inhibition of acetylcholinesterase (AChE), CPF has the ability to exert toxicity on non-target species in aquatic systems. In fish species, exposure to CPF has been associated with a range of adverse effects across physiological endpoints including abnormal development, inhibition of AChE, immunomodulation, and molecular level effects such as altered expression of specific genes and global transcriptomes. However, the literature on amphibians exposed to CPF is not as extensive despite the known global declines of amphibian species and the hypothesized links between these declines and anthropogenic pesticide contamination of aquatic systems worldwide. The overall objective of this thesis was to gain a better understanding of the sub-lethal effects of CPF exposure on the model amphibian, Xenopus laevis, across levels of biological organization from molecular to whole animal. 
-The first study (Chapter 2) examined the molecular toxicity pathways and mechanisms of toxicity after short-term exposure of early life-stage (ELS) X. laevis to CPF using whole body transcriptome analyses. The ELS transcriptomic responses were then compared to apical outcomes of chronic exposure to CPF to determine if identified dysregulated pathways could provide early indicators of these adverse outcomes. Post-hatch individuals were exposed to nominal CPF concentrations of 0.4, 2, or 10 μg L-1. A subset of individuals were sampled at 96 hours (h) for whole-body transcriptomic analysis and remaining individuals were transferred to tanks for long-term exposure through to metamorphic climax ({\textasciitilde} 75 days). Pathway analysis revealed dysregulated pathways that were related to outcomes known to be associated with exposure to CPF such as altered serine hydrolase activity, impacted metabolic processes, and immune-related outcomes. Other dysregulated pathways with less precedence in the literature included vasculature development and sensory perception of light stimulus. Apical outcomes of chronic CPF exposure included inhibition of AChE activity, increased relative liver weight, and a decrease in percentage of individuals that reached metamorphic climax. Dysregulation of serine hydrolase associated pathways after ELS CPF exposure is in agreeance with the decrease in AChE (a serine hydrolase enzyme) activity observed in the brains of individuals at metamorphic climax. Additionally, an increase in relative liver weight after chronic CPF exposure could be related to dysregulation of ELS pathways associated with metabolic processes and immune function. In fact, several pathways related to immune function were depleted.
-In Chapter 3, we more closely examined the potential immunotoxicity of sub-lethal CPF exposure. Post-metamorphic individuals were exposed 1 or 10 μg L-1 CPF (nominal) for 7 days (d), then administered a phosphate buffered sodium (PBS) control injection or a lipopolysaccharide (LPS) injection to stimulate an inflammatory response. At 24 h post-injection, morphometric indices were recorded and tissues were sampled for differential leukocyte counts (flow cytometry), liver pro-inflammatory cytokine expression (qPCR), and kidney histopathology. At 1 µg L−1 CPF, there was a decrease in circulating lymphocytes, an increase in circulating granulocytes, and an increase in the granulocyte:lymphocyte (GL) ratio regardless of immune state. Liver expression of pro-inflammatory cytokines TNF-α and CSF-1 was increased in individuals exposed to 10 µg L−1 CPF, independent of immune state. Exposure to 10 μg L-1 CPF increased kidney epithelial cell height (by 18 \%) and decreased lumen space in the convoluted tubules of the kidney. This study provided evidence that exposure to CPF can lead to changes in key biomarkers of immune status in amphibians in both immune-rested (PBS-injected) and immune-stimulated (LPS-injected) states. Additionally, we found that LPS was an effective mitogen in our study, capable of inducing a robust and measurable stress response in X. laevis. This response included a decrease in circulating lymphocytes, and increase in circulating monocytes, and an increase in the GL ratio. In addition, increased liver expression of pro-inflammatory cytokines TNF-α, IL-1β, and CSF-1 was induced by LPS injection. We conclude that LPS is an appropriate immunostimulatory agent in an immune challenge assay using X. laevis and that exposure to CPF does not appear to impact the response to LPS exposure. 
-Overall, our findings show that exposure to environmentally relevant concentrations of CPF has the ability to impact amphibians at multiple levels of biological organization. A number of affected molecular pathways warrant further study in terms of the underlying mechanisms of CPF-mediated toxicity as well as the associated outcomes of CPF exposure in amphibians. This research provides novel data on the effects of CPF exposure to amphibians, which are generally overlooked and under-represented in the literature despite links between pesticide exposure and globally declining amphibian populations.},
- author = {Baldwin, Nicole Perras 1993-},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- school = {University of Saskatchewan},
- title = {{EVALUATING} {THE} {SUB}-{LETHAL} {TOXICITY} {OF} {THE} {ORGANOPHOSPHATE} {PESTICIDE}, {CHLORPYRIFOS}, {ON} {THE} {AMPHIBIAN}, {XENOPUS} {LAEVIS}},
- type = {Thesis},
- url = {https://harvest.usask.ca/handle/10388/12429},
- urldate = {2019-11-26},
- year = {2019}
-}
-
-@article{bamford_collaboration_2021,
- author = {Bamford, Connor G. G. and Broadbent, Lindsay and Aranday-Cortes, Elihu and McCabe, Mary and McKenna, James and Courtney, David and Touzelet, Olivier and Ali, Ahlam and Roberts, Grace and Campos, Guillermo Lopez and Simpson, David and McCaughey, Conall and Fairley, Derek and Mills, Ken and and, Ultan F. Power},
- doi = {10.1101/2021.07.16.452629},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Collaboration {Between} {Host} and {Viral} {Factors} {Shape} {SARS}-{CoV}-2 {Evolution}},
- url = {https://doi.org/10.1101/2021.07.16.452629},
- year = {2021}
-}
-
-@article{bamford_comparison_2022,
- author = {Bamford, Connor G. G. and Broadbent, Lindsay and Aranday-Cortes, Elihu and McCabe, Mary and McKenna, James and Courtney, David G. and Touzelet, Olivier and Ali, Ahlam and Roberts, Grace and Campos, Guillermo Lopez and Simpson, David and McCaughey, Conall and Fairley, Derek and Mills, Ken and and, Ultan F. Power},
- doi = {10.3390/v14020325},
- journal = {Viruses},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: MDPI AG},
- number = {2},
- pages = {325},
- title = {Comparison of {SARS}-{CoV}-2 {Evolution} in {Paediatric} {Primary} {Airway} {Epithelial} {Cell} {Cultures} {Compared} with {Vero}-{Derived} {Cell} {Lines}},
- url = {https://doi.org/10.3390/v14020325},
- volume = {14},
- year = {2022}
-}
-
-@article{bandyopadhyay_polypharmacology_2021,
- author = {Bandyopadhyay, Suritra and Abiodun, Omobolanle Abimbola and Ogboo, Blessing Chinweotito and Kola-Mustapha, Adeola Tawakalitu and Attah, Emmanuel Ifeanyi and Edemhanria, Lawrence and Kumari, Ankita and Jaganathan, Ravindran and Adelakun, Niyi S.},
- doi = {10.1080/07391102.2021.1959401},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Informa UK Limited},
- pages = {1--17},
- title = {Polypharmacology of some medicinal plant metabolites against {SARS}-{CoV}-2 and host targets: {Molecular} dynamics evaluation of {NSP9} {RNA} binding protein},
- url = {https://doi.org/10.1080/07391102.2021.1959401},
- year = {2021}
-}
-
-@article{barbosa_new_2021,
- author = {Barbosa, David Aciole and Simeone, Alexandre Santos and Humberto, Ana Carolina and Maria, Yara Natercia Lima Faustino de and Oliveira, Regina Costa de and Jabes, Daniela L. and Nunes, Luiz R. and Menegidio, Fabiano Bezerra},
- doi = {10.21203/rs.3.rs-1050608/v1},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {November},
- note = {Publisher: Research Square Platform LLC},
- title = {New {Putative} {Long} {Non}-{Coding} {RNAs} ({lncRNA}) {Revealed} by {Pan}-{Transcriptome} of the {Emerging} {Human} {Pathogenic} {Fungus} {Talaromyces} {Marneffei}},
- url = {https://doi.org/10.21203/rs.3.rs-1050608/v1},
- year = {2021}
-}
-
-@article{baron_multidrug-resistant_2021,
- author = {Baron, Sophie Alexandra and Mediannikov, Oleg and Abdallah, Rim and Yimagou, Edmond Kuete and Medkour, Hacène and Dubourg, Gregory and Elamire, Youssouf and Afouda, Pamela and Ngom, Issa Isaac and Angelakis, Emmanouil and Davoust, Bernard and Diatta, Georges and Barciela, Amanda and Hernandez-Aguilar, R. Adriana and Sokhna, Cheikh and Caputo, Aurelia and Levasseur, Anthony and Rolain, Jean-Marc and Raoult, Didier},
- doi = {10.1128/aac.02557-20},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: American Society for Microbiology},
- number = {9},
- title = {Multidrug-{Resistant} {Klebsiella} pneumoniae {Clones} from {Wild} {Chimpanzees} and {Termites} in {Senegal}},
- url = {https://doi.org/10.1128/aac.02557-20},
- volume = {65},
- year = {2021}
-}
-
-@article{barragan-rosillo_genome_2021,
- author = {Barragán-Rosillo, Alfonso Carlos and Peralta-Alvarez, Carlos Alberto and Ojeda-Rivera, Jonathan Odilón and Arzate-Mejía, Rodrigo G. and Recillas-Targa, Félix and Herrera-Estrella, Luis},
- doi = {10.1073/pnas.2107558118},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Proceedings of the National Academy of Sciences},
- number = {33},
- pages = {e2107558118},
- title = {Genome accessibility dynamics in response to phosphate limitation is controlled by the {PHR1} family of transcription factors in {Arabidopsis}},
- url = {https://doi.org/10.1073/pnas.2107558118},
- volume = {118},
- year = {2021}
-}
-
-@article{bartas_changes_2021,
- author = {Bartas, Martin and Brázda, Václav and Volná, Adriana and Červeň, Jiří and Pečinka, Petr and Zawacka-Pankau, Joanna E.},
- doi = {10.3390/ijms22168512},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: MDPI AG},
- number = {16},
- pages = {8512},
- title = {The {Changes} in the p53 {Protein} across the {Animal} {Kingdom} {Point} to {Its} {Involvement} in {Longevity}},
- url = {https://doi.org/10.3390/ijms22168512},
- volume = {22},
- year = {2021}
-}
-
-@article{batut_asaim_2018,
- author = {Batut, Bérénice and Gravouil, Kevin and Defois, Clemence and Hiltemann, Saskia and Brugère, Jean-François and Peyretaillade, Eric and Peyret, Pierre},
- journal = {GigaScience},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Oxford University Press},
- number = {6},
- pages = {giy057},
- title = {{ASaiM}: a {Galaxy}-based framework to analyze microbiota data},
- volume = {7},
- year = {2018}
-}
-
-@article{batut_asaim_2018-1,
- abstract = {Background.  New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics a},
- author = {Batut, Bérénice and Gravouil, Kévin and Defois, Clémence and Hiltemann, Saskia and Brugère, Jean-François and Peyretaillade, Eric and Peyret, Pierre},
- doi = {10.1093/gigascience/giy057},
- journal = {GigaScience},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}ASaiM, {\textgreater}Metagenomics EU},
- language = {en},
- month = {June},
- number = {6},
- shorttitle = {{ASaiM}},
- title = {{ASaiM}: a {Galaxy}-based framework to analyze microbiota data},
- url = {https://academic.oup.com/gigascience/article/7/6/giy057/5001424},
- urldate = {2018-07-12},
- volume = {7},
- year = {2018}
-}
-
-@article{batut_community-driven_2018,
- abstract = {The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.},
- author = {Batut, Bérénice and Hiltemann, Saskia and Bagnacani, Andrea and Baker, Dannon and Bhardwaj, Vivek and Blank, Clemens and Bretaudeau, Anthony and Brillet-Guéguen, Loraine and Čech, Martin and Chilton, John and Clements, Dave and Doppelt-Azeroual, Olivia and Erxleben, Anika and Freeberg, Mallory Ann and Gladman, Simon and Hoogstrate, Youri and Hotz, Hans-Rudolf and Houwaart, Torsten and Jagtap, Pratik and Larivière, Delphine and Corguillé, Gildas Le and Manke, Thomas and Mareuil, Fabien and Ramírez, Fidel and Ryan, Devon and Sigloch, Florian Christoph and Soranzo, Nicola and Wolff, Joachim and Videm, Pavankumar and Wolfien, Markus and Wubuli, Aisanjiang and Yusuf, Dilmurat and Taylor, James and Backofen, Rolf and Nekrutenko, Anton and Grüning, Björn},
- doi = {10.1016/j.cels.2018.05.012},
- issn = {2405-4712},
- journal = {Cell Systems},
- keywords = {+Education, +Galactic, +RefPublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, data analysis, genomics, next-generation sequencing, proteomics, training},
- language = {English},
- month = {June},
- number = {6},
- pages = {752--758.e1},
- pmid = {29953864},
- title = {Community-{Driven} {Data} {Analysis} {Training} for {Biology}},
- url = {https://www.cell.com/cell-systems/abstract/S2405-4712(18)30230-8},
- urldate = {2018-07-16},
- volume = {6},
- year = {2018}
-}
-
-@incollection{batut_rna-seq_2021,
- abstract = {A complete RNA-Seq analysis involves the use of several different tools, with substantial software and computational requirements. The Galaxy platform simplifies the execution of such bioinformatics analyses by embedding the needed tools in its web interface, while also providing reproducibility. Here, we describe how to perform a reference-based RNA-Seq analysis using Galaxy, from data upload to visualization and functional enrichment analysis of differentially expressed genes.},
- address = {New York, NY},
- author = {Batut, Bérénice and van den Beek, Marius and Doyle, Maria A. and Soranzo, Nicola},
- booktitle = {{RNA} {Bioinformatics}},
- doi = {10.1007/978-1-0716-1307-8_20},
- editor = {Picardi, Ernesto},
- isbn = {978-1-07-161307-8},
- keywords = {+Galactic, +HowTo, +IsGalaxy, +RefPublic, {\textgreater}UseGalaxy.eu, Differential gene expression, Functional enrichment, Galaxy, Quality control, Sequence mapping, Visualizations, Workflow},
- language = {en},
- pages = {367--392},
- publisher = {Springer US},
- series = {Methods in {Molecular} {Biology}},
- title = {{RNA}-{Seq} {Data} {Analysis} in {Galaxy}},
- url = {https://doi.org/10.1007/978-1-0716-1307-8_20},
- urldate = {2021-04-13},
- year = {2021}
-}
-
-@article{bauer_functional_2021,
- author = {Bauer, Tabea L. and Collmar, Katrin and Kaltofen, Till and Loeffler, Ann-Katrin and Decker, Lorena and Mueller, Jan and Pinter, Sabine and Eisler, Stephan A. and Mahner, Sven and Fraungruber, Patricia and Kommoss, Stefan and Staebler, Annette and Francis, Lewis and Conlan, R. Steven and Zuber, Johannes and Jeschke, Udo and Trillsch, Fabian and Rathert, Philipp},
- doi = {10.3390/cancers13153801},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: MDPI AG},
- number = {15},
- pages = {3801},
- title = {Functional {Analysis} of {Non}-{Genetic} {Resistance} to {Platinum} in {Epithelial} {Ovarian} {Cancer} {Reveals} a {Role} for the {MBD3}-{NuRD} {Complex} in {Resistance} {Development}},
- url = {https://doi.org/10.3390/cancers13153801},
- volume = {13},
- year = {2021}
-}
-
-@article{bayona-feliu_swisnf_2021,
- author = {Bayona-Feliu, Aleix and Barroso, Sonia and Muñoz, Sergio and Aguilera, Andrés},
- doi = {10.1038/s41588-021-00867-2},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {May},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {7},
- pages = {1050--1063},
- title = {The {SWI}/{SNF} chromatin remodeling complex helps resolve {R}-loop-mediated transcription–replication conflicts},
- url = {https://doi.org/10.1038/s41588-021-00867-2},
- volume = {53},
- year = {2021}
-}
-
-@article{bazzucchi_near-complete_2020,
- abstract = {To gain further insight into the genomic features of border disease virus (BDV), we determined the nearly complete genome sequence of isolate TO/121/04 from an aborted ovine fetus. Its genome contains a single open reading frame (ORF), which comprises 11,681 nucleotides encoding a polyprotein of 3893 amino acids. Phylogenetic analysis of the near full-length genome sequence showed that the BDV isolate differed significantly from all ovine pestiviruses identified so far, thus re-affirming the presence in Italy of this novel genetic group, termed BDV-7.},
- author = {Bazzucchi, Moira and Pierini, Ilaria and Giammarioli, Monica and De Mia, Gian Mario},
- doi = {10.1007/s00705-020-04836-8},
- issn = {1432-8798},
- journal = {Archives of Virology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- number = {12},
- pages = {3007--3009},
- title = {Near-complete nucleotide sequence of a border disease virus genotype {BDV}-7 isolate from {Italy}},
- url = {https://doi.org/10.1007/s00705-020-04836-8},
- urldate = {2021-04-14},
- volume = {165},
- year = {2020}
-}
-
-@article{blacklock_examination_2022,
- author = {Blacklock, Emily},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- title = {Examination of crustacean immune responses through {dsRNA}-nanoparticle injection and phylogenetic analysis},
- year = {2022}
-}
-
-@article{blagitko-dorfs_combination_2018,
- abstract = {DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2′-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi. Transcriptome analyses revealed that a combined treatment with DAC and the HDACi panobinostat or valproic acid affected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative methylome and transcriptome analyses showed that a massive downregulation of genes, including oncogenes (e.g., MYC) and epigenetic modifiers (e.g., KDM2B, SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatments, and for a better understanding of responses in trials where this approach is clinically tested.},
- author = {Blagitko-Dorfs, Nadja and Schlosser, Pascal and Greve, Gabriele and Pfeifer, Dietmar and Meier, Ruth and Baude, Annika and Brocks, David and Plass, Christoph and Lübbert, Michael},
- copyright = {2018 Springer Nature Limited},
- doi = {10.1038/s41375-018-0293-8},
- issn = {1476-5551},
- journal = {Leukemia},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {En},
- month = {November},
- pages = {1},
- shorttitle = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors},
- title = {Combination treatment of acute myeloid leukemia cells with {DNMT} and {HDAC} inhibitors: predominant synergistic gene downregulation associated with gene body demethylation},
- url = {https://www.nature.com/articles/s41375-018-0293-8},
- urldate = {2018-11-29},
- year = {2018}
-}
-
-@article{blomberg_connecting_2020,
- abstract = {ELIXIR, the European research infrastructure for life science data, provides open access to data, tools and workflows in the response to the COVID-19 pandemic. ELIXIR’s 23 nodes have reacted swiftly to support researchers in their combined efforts against the pandemic setting out three joint priorities: 1. Connecting national COVID-19 data platforms to create federated European COVID-19 Data Spaces; 2. Fostering good data management to make COVID-19 data open, FAIR and reusable over the long term; 3. Providing open tools, workflows and computational resources to drive reproducible and collaborative science. ELIXIR’s strategy is based on the support given by our national nodes - collectively spanning over 200 institutes - to research projects and on partnering with community initiatives to drive development and adoption of good data practice and community driven standards. ELIXIR Nodes provide support activities locally and internationally, from provisioning compute capabilities to helping collect viral sequence data from hospitals. Some Nodes have prioritised access to their national cloud and compute facilities for all COVID-19 research projects, while others have developed tools to search, access and share all data related to the pandemic in a national healthcare setting.},
- author = {Blomberg, Niklas and Lauer, Katharina B.},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41431-020-0637-5},
- issn = {1476-5438},
- journal = {European Journal of Human Genetics},
- keywords = {+RefPublic, +Stellar, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Nature Publishing Group},
- pages = {1--5},
- shorttitle = {Connecting data, tools and people across {Europe}},
- title = {Connecting data, tools and people across {Europe}: {ELIXIR}’s response to the {COVID}-19 pandemic},
- url = {https://www.nature.com/articles/s41431-020-0637-5},
- urldate = {2020-05-22},
- year = {2020}
-}
-
-@article{bohlender_stable_2020,
- abstract = {Recombinantly produced proteins are indispensable tools for medical applications. Since the majority of them are glycoproteins, their N-glycosylation profiles are major determinants for their activity, structural properties and safety. For therapeutical applications, a glycosylation pattern adapted to product and treatment requirements is advantageous. Physcomitrium patens (Physcomitrella, moss) is able to perform highly homogeneous complex-type N-glycosylation. Additionally, it has been glyco-engineered to eliminate plant-specific sugar residues by knock-out of the β1,2-xylosyltransferase and α1,3-fucosyltransferase genes (Δxt/ft). Furthermore, Physcomitrella meets wide-ranging biopharmaceutical requirements such as GMP compliance, product safety, scalability and outstanding possibilities for precise genome engineering. However, all plants, in contrast to mammals, lack the capability to perform N-glycan sialylation. Since sialic acids are a common terminal modification on human N glycans, the property to perform N-glycan sialylation is highly desired within the plant-based biopharmaceutical sector. In this study, we present the successful achievement of protein N-glycan sialylation in stably transformed Physcomitrella. The sialylation ability was achieved in a Δxt/ft moss line by stable expression of seven mammalian coding sequences combined with targeted organelle-specific localization of the encoded enzymes responsible for the generation of β1,4 galactosylated acceptor N glycans as well as the synthesis, activation, transport and transfer of sialic acid. Production of free (Neu5Ac) and activated (CMP-Neu5Ac) sialic acid was proven. The glycosidic anchor for the attachment of terminal sialic acid was generated by the introduction of a chimeric human β1,4 galactosyltransferase gene under the simultaneous knock-out of the gene encoding the endogenous β1,3 galactosyltransferase. Functional complex-type N-glycan sialylation was confirmed via mass spectrometric analysis of a stably co-expressed recombinant human protein.},
- author = {Bohlender, Lennard L. and Parsons, Juliana and Hoernstein, Sebastian N. W. and Rempfer, Christine and Ruiz-Molina, Natalia and Lorenz, Timo and Rodríguez Jahnke, Fernando and Figl, Rudolf and Fode, Benjamin and Altmann, Friedrich and Reski, Ralf and Decker, Eva L.},
- doi = {10.3389/fpls.2020.610032},
- issn = {1664-462X},
- journal = {Frontiers in Plant Science},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Glyco-engineering, N-glycan humanization, N-glycan sialylation, PMP, glyco-optimization, plant-made pharmaceuticals, plant-made recombinant biopharmaceuticals},
- language = {English},
- note = {Publisher: Frontiers},
- title = {Stable {Protein} {Sialylation} in {Physcomitrella}},
- url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.610032/full},
- urldate = {2021-05-12},
- volume = {11},
- year = {2020}
-}
-
-@article{boneva_3_2020,
- abstract = {This study aims to compare the potential of standard RNA-sequencing (RNA-Seq) and 3′ massive analysis of c-DNA ends (MACE) RNA-sequencing for the analysis of fresh tissue and describes transcriptome profiling of formalin-fixed paraffin-embedded (FFPE) archival human samples by MACE. To compare MACE to standard RNA-Seq on fresh tissue, four healthy conjunctiva from four subjects were collected during vitreoretinal surgery, halved and immediately transferred to RNA lysis buffer without prior fixation and then processed for either standard RNA-Seq or MACE RNA-Seq analysis. To assess the impact of FFPE preparation on MACE, a third part was fixed in formalin and processed for paraffin embedding, and its transcriptional profile was compared with the unfixed specimens analyzed by MACE. To investigate the impact of FFPE storage time on MACE results, 24 FFPE-treated conjunctival samples from 24 patients were analyzed as well. Nineteen thousand six hundred fifty-nine transcribed genes were detected by both MACE and standard RNA-Seq on fresh tissue, while 3251 and 2213 transcripts were identified explicitly by MACE or RNA-Seq, respectively. Standard RNA-Seq tended to yield longer detected transcripts more often than MACE technology despite normalization, indicating that the MACE technology is less susceptible to a length bias. FFPE processing revealed negligible effects on MACE sequencing results. Several quality-control measurements showed that long-term storage in paraffin did not decrease the diversity of MACE libraries. We noted a nonlinear relation between storage time and the number of raw reads with an accelerated decrease within the first 1000 days in paraffin, while the numbers remained relatively stable in older samples. Interestingly, the number of transcribed genes detected was independent on FFPE storage time. RNA of sufficient quality and quantity can be extracted from FFPE samples to obtain comprehensive transcriptome profiling using MACE technology. We thus present MACE as a novel opportunity for utilizing FFPE samples stored in histological archives.},
- author = {Boneva, Stefaniya and Schlecht, Anja and Böhringer, Daniel and Mittelviefhaus, Hans and Reinhard, Thomas and Agostini, Hansjürgen and Auw-Haedrich, Claudia and Schlunck, Günther and Wolf, Julian and Lange, Clemens},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41374-020-0446-z},
- issn = {1530-0307},
- journal = {Laboratory Investigation},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Nature Publishing Group},
- pages = {1--11},
- title = {3′ {MACE} {RNA}-sequencing allows for transcriptome profiling in human tissue samples after long-term storage},
- url = {https://www.nature.com/articles/s41374-020-0446-z},
- urldate = {2020-08-12},
- year = {2020}
-}
-
-@article{boneva_mace_2020,
- abstract = {Recent advances in the field of biomedical research allow for elucidation of the transcriptional signature of rare tumors such as conjunctival squamous cell carcinoma (SCC). In this study we compare its expression profile to conjunctival papilloma (Pap) and healthy conjunctival tissue (Ctrl) and develop a classification tool to differentiate these entities. Seven conjunctival SCC, seven Pap and ten Ctrl were formalin-fixed and paraffin-embedded (FFPE) and analyzed using Massive Analysis of cDNA Ends (MACE) RNA sequencing. Differentially expressed genes (DEG) and gene ontology (GO) clusters were explored and the abundance of involved cell types was quantified by xCell. Finally, a classification model was developed to distinguish SCC from Pap and Ctrl. Among the most prominent DEG in SCC a plethora of keratins were upregulated when compared to Pap and Ctrl. xCell analysis revealed an enrichment of immune cells, including activated dendritic cells and T-helper type 1 cells (Th1), in SCC when compared to Ctrl. The generated classification model could reliably discriminate between the three entities according to the expression pattern of 30 factors. This study provides a transcriptome-wide gene expression profile of rare conjunctival SCC. The analysis identifies distinct keratins, as well as dendritic and Th1 cells as important mediators in SCC. Finally, the provided gene expression classifier may become an aid to the conventional histological classification of conjunctival tumors in uncertain cases.},
- author = {Boneva, Stefaniya and Schlecht, Anja and Zhang, Peipei and Boehringer, Daniel and Lapp, Thabo and Mittelviefhaus, Hans and Reinhard, Thomas and Auw-Haedrich, Claudia and Schlunck, Guenther and Wolf, Julian and Lange, Clemens},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-78339-6},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {21292},
- title = {{MACE} {RNA} sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue},
- url = {https://www.nature.com/articles/s41598-020-78339-6},
- urldate = {2021-04-08},
- volume = {10},
- year = {2020}
-}
-
-@article{boneva_transcriptional_2020,
- abstract = {To decipher the transcriptional signature of macrophages of the human vitreous, also known as hyalocytes, and compare it to the profiles of other myeloid cell populations including human blood-derived monocytes, macrophages and brain microglia. This study involves a total of 13 patients of advanced age with disorders of the vitreoretinal interface undergoing vitrectomy at the University Eye Hospital Freiburg between 2018 and 2019. Vitreal hyalocytes were analyzed by fluorescence-activated cell sorting (FACS) and isolated as CD45+CD11b+CX3CR1+Mat-Mac+ cells using a FACS-based sorting protocol. RNA extraction, library preparation and RNA sequencing were performed and the sequencing data was analyzed using the Galaxy web platform. The transcriptome of human hyalocytes was compared to the transcriptional profile of human blood-derived monocytes, macrophages and brain microglia obtained from public databases. Protein validation for selected factors was performed by immunohistochemistry on paraffin sections from three human donor eyes. On average, 383 ± 233 hyalocytes were isolated per patient, resulting in 128 pg/µl ± 76 pg/µl total RNA per sample. RNA sequencing revealed that SPP1, FTL, CD74 and HLA-DRA are among the most abundantly expressed genes in hyalocytes, which was confirmed by immunofluorescence for CD74, FTL and HLA-DRA. Gene ontology (GO) enrichment analysis showed that biological processes such as “humoral immune response”, “leukocyte migration” and “antigen processing and presentation of peptide antigen” (adjusted p \< 0.001) are dominating in vitreal hyalocytes. While the comparison of the gene expression profiles of hyalocytes and other myeloid cell populations showed an overall strong similarity (R2 \> 0.637, p \< 0.001), hyalocytes demonstrated significant differences with respect to common leukocyte-associated factors. In particular, transcripts involved in the immune privilege of the eye, such as POMC, CD46 and CD86, were significantly increased in hyalocytes compared to other myeloid cell subsets. Human hyalocytes represent a unique and distinct innate immune cell population specialized and adapted for the tissue-specific needs in the human vitreous. Vitreal hyalocytes are characterized by a strong expression of genes related to antigen processing and presentation as well as immune modulation. Thus, hyalocytes may represent an underestimated mediator in vitreoretinal disease and for the immune privilege of the eye.},
- author = {Boneva, Stefaniya Konstantinova and Wolf, Julian and Rosmus, Dennis-Dominik and Schlecht, Anja and Prinz, Gabriele and Laich, Yannik and Boeck, Myriam and Zhang, Peipei and Hilgendorf, Ingo and Stahl, Andreas and Reinhard, Thomas and Bainbridge, James and Schlunck, Günther and Agostini, Hansjürgen and Wieghofer, Peter and Lange, Clemens A. K.},
- doi = {10.3389/fimmu.2020.567274},
- issn = {1664-3224},
- journal = {Frontiers in Immunology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Hyalocytes, Immune Privilege, Myeloid Cells, Viterous Body, Vitreous Macrophages, innate immunity},
- language = {English},
- note = {Publisher: Frontiers},
- title = {Transcriptional {Profiling} {Uncovers} {Human} {Hyalocytes} as a {Unique} {Innate} {Immune} {Cell} {Population}},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.567274/full},
- urldate = {2021-05-15},
- volume = {11},
- year = {2020}
-}
-
-@article{bose_trna_2020,
- abstract = {tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism.},
- author = {Bose, Sreyashree and Suescún, Ana Victoria and Song, Jiarui and Castillo-González, Claudia and Aklilu, Behailu Birhanu and Branham, Erica and Lynch, Ryan and Shippen, Dorothy E.},
- doi = {10.1007/s00299-020-02594-0},
- issn = {1432-203X},
- journal = {Plant Cell Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- number = {12},
- pages = {1669--1685},
- title = {{tRNA} {ADENOSINE} {DEAMINASE} 3 is required for telomere maintenance in {Arabidopsis} thaliana},
- url = {https://doi.org/10.1007/s00299-020-02594-0},
- urldate = {2021-05-15},
- volume = {39},
- year = {2020}
-}
-
-@article{bossche_critical_2021,
- abstract = {{\textless}p{\textgreater}Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample. We observed that variability at the peptide level was predominantly due to wet-lab workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-lab studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.{\textless}/p{\textgreater}},
- author = {Bossche, Tim Van Den and Kunath, Benoit J. and Schallert, Kay and Schäpe, Stephanie S. and Abraham, Paul E. and Armengaud, Jean and Arntzen, Magnus Ø and Bassignani, Ariane and Benndorf, Dirk and Fuchs, Stephan and Giannone, Richard J. and Griffin, Timothy J. and Hagen, Live H. and Halder, Rashi and Henry, Céline and Hettich, Robert L. and Heyer, Robert and Jagtap, Pratik and Jehmlich, Nico and Jensen, Marlene and Juste, Catherine and Kleiner, Manuel and Langella, Olivier and Lehmann, Theresa and Leith, Emma and May, Patrick and Mesuere, Bart and Miotello, Guylaine and Peters, Samantha L. and Pible, Olivier and Reichl, Udo and Renard, Bernhard Y. and Schiebenhoefer, Henning and Scryba, Alexander and Tanca, Alessandro and Trappe, Kathrin and Trezzi, Jean-Pierre and Uzzau, Sergio and Verschaffelt, Pieter and Bergen, Martin von and Wilmes, Paul and Wolf, Maximilian and Martens, Lennart and Muth, Thilo},
- copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
- doi = {10.1101/2021.03.05.433915},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2021.03.05.433915},
- shorttitle = {Critical {Assessment} of {Metaproteome} {Investigation} ({CAMPI})},
- title = {Critical {Assessment} of {Metaproteome} {Investigation} ({CAMPI}): {A} {Multi}-{Lab} {Comparison} of {Established} {Workflows}},
- url = {https://www.biorxiv.org/content/10.1101/2021.03.05.433915v1},
- urldate = {2021-03-08},
- year = {2021}
-}
-
-@article{bovio_differential_2018,
- abstract = {The disruptor of telomeric silencing 1-like (DOT1L) mediates methylation of histone H3 at position lysine 79 (H3K79). Conditional knockout of Dot1l in mouse cerebellar granule cells (Dot1l-cKOAtoh1) led to a smaller external granular layer with fewer precursors of granule neurons. Dot1l-cKOAtoh1 mice had impaired proliferation and differentiation of granular progenitors, which resulted in a smaller cerebellum. Mutant mice showed mild ataxia in motor behavior tests. In contrast, Purkinje cell-specific conditional knockout mice showed no obvious phenotype. Genome-wide transcription analysis of Dot1l-cKOAtoh1 cerebella using microarrays revealed changes in genes that function in cell cycle, cell migration, axon guidance, and metabolism. To identify direct DOT1L target genes, we used genome-wide profiling of H3K79me2 and transcriptional analysis. Analysis of differentially methylated regions (DR) and differentially expressed genes (DE) revealed in total 12 putative DOT1L target genes in Dot1l-cKOAtoh1 affecting signaling (Tnfaip8l3, B3galt5), transcription (Otx1), cell migration and axon guidance (Sema4a, Sema5a, Robo1), cholesterol and lipid metabolism (Lss, Cyp51), cell cycle (Cdkn1a), calcium-dependent cell-adhesion or exocytosis (Pcdh17, Cadps2), and unknown function (Fam174b). Dysregulated expression of these target genes might be implicated in the ataxia phenotype observed in Dot1l-cKOAtoh1.},
- author = {Bovio, Patrick Piero and Franz, Henriette and Heidrich, Stefanie and Rauleac, Tudor and Kilpert, Fabian and Manke, Thomas and Vogel, Tanja},
- doi = {10.1007/s12035-018-1377-1},
- issn = {1559-1182},
- journal = {Molecular Neurobiology},
- keywords = {+Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu, Ataxia, Atoh1, Epigenetics, Purkinje cell},
- language = {en},
- month = {October},
- title = {Differential {Methylation} of {H3K79} {Reveals} {DOT1L} {Target} {Genes} and {Function} in the {Cerebellum} {In} {Vivo}},
- url = {https://doi.org/10.1007/s12035-018-1377-1},
- urldate = {2018-10-18},
- year = {2018}
-}
-
-@article{bray_chemicaltoolbox_2020,
- abstract = {Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows may be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project. The ChemicalToolbox is hosted on the European Galaxy server and may be accessed via https://cheminformatics.usegalaxy.eu.},
- author = {Bray, Simon A. and Lucas, Xavier and Kumar, Anup and Grüning, Björn A.},
- doi = {10.1186/s13321-020-00442-7},
- issn = {1758-2946},
- journal = {Journal of Cheminformatics},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}ChemicalToolbox},
- month = {June},
- number = {1},
- pages = {40},
- shorttitle = {The {ChemicalToolbox}},
- title = {The {ChemicalToolbox}: reproducible, user-friendly cheminformatics analysis on the {Galaxy} platform},
- url = {https://doi.org/10.1186/s13321-020-00442-7},
- urldate = {2020-06-05},
- volume = {12},
- year = {2020}
-}
-
-@article{bray_galaxy_2021,
- abstract = {We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 40000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.},
- author = {Bray, Simon and Dudgeon, Tim and Skyner, Rachael and Backofen, Rolf and Grüning, Björn and Delft, Frank von},
- doi = {10.26434/chemrxiv-2021-zr4xn},
- journal = {ChemRxiv},
- keywords = {+Galactic, +IsGalaxy, +Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- shorttitle = {Galaxy workflows for fragment-based virtual screening},
- title = {Galaxy workflows for fragment-based virtual screening: a case study on the {SARS}-{CoV}-2 main protease},
- url = {https://chemrxiv.org/engage/chemrxiv/article-details/61a621c1ceb7d316bd010728},
- urldate = {2021-12-07},
- year = {2021}
-}
-
-@article{bray_intuitive_2020,
- abstract = {This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible and transparent process. In this tutorial we focus on 3 questions: How are protein-ligand systems parameterized for molecular dynamics simulation? What kind of analysis can be carried out on molecular trajectories? How can high-throughput MD be used to study multiple ligands? After finishing you will have learned about force-fields and MD parameterization, how to conduct MD simulation and analysis for a protein-ligand system, and understand how different molecular interactions contribute to the binding affinity of ligands to the Hsp90 protein.},
- author = {Bray, Simon A. and Senapathi, Tharindu and Barnett, Christopher B. and Grüning, Björn A.},
- doi = {10.1186/s13321-020-00451-6},
- issn = {1758-2946},
- journal = {Journal of Cheminformatics},
- keywords = {+Galactic, +HowTo, +IsGalaxy, +Shared, {\textgreater}BRIDGE, {\textgreater}ChemicalToolbox, Galaxy, Molecular Dynamics, Reproducible},
- month = {September},
- number = {1},
- pages = {54},
- shorttitle = {Intuitive, reproducible high-throughput molecular dynamics in {Galaxy}},
- title = {Intuitive, reproducible high-throughput molecular dynamics in {Galaxy}: a tutorial},
- url = {https://doi.org/10.1186/s13321-020-00451-6},
- urldate = {2021-04-07},
- volume = {12},
- year = {2020}
-}
-
-@article{broche_genome-wide_2021,
- abstract = {Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90\% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.},
- author = {Broche, Julian and Kungulovski, Goran and Bashtrykov, Pavel and Rathert, Philipp and Jeltsch, Albert},
- doi = {10.1093/nar/gkaa1169},
- issn = {0305-1048},
- journal = {Nucleic Acids Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- number = {1},
- pages = {158--176},
- title = {Genome-wide investigation of the dynamic changes of epigenome modifications after global {DNA} methylation editing},
- url = {https://doi.org/10.1093/nar/gkaa1169},
- urldate = {2021-02-18},
- volume = {49},
- year = {2021}
-}
-
-@article{brunet_mass_2019,
- abstract = {Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame (ORF) annotation impose two arbitrary criteria: a minimum length of 100 codons and a single ORF per transcript. However, a growing number of studies report expression of proteins from allegedly non-coding regions, challenging the accuracy of current genome annotations. These novel proteins were found encoded either within non-coding RNAs, 5' or 3' untranslated regions (UTRs) of mRNAs, or overlapping a known coding sequence (CDS) in an alternative ORF. OpenProt is the first database that enforces a polycistronic model for eukaryotic genomes, allowing annotation of multiple ORFs per transcript. OpenProt is freely accessible and offers custom downloads of protein sequences across 10 species. Using OpenProt database for proteomic experiments enables novel proteins discovery and highlights the polycistronic nature of eukaryotic genes. The size of OpenProt database (all predicted proteins) is substantial and need be taken in account for the analysis. However, with appropriate false discovery rate (FDR) settings or the use of a restricted OpenProt database, users will gain a more realistic view of the proteomic landscape. Overall, OpenProt is a freely available tool that will foster proteomic discoveries.},
- author = {Brunet, Marie A. and Roucou, Xavier},
- doi = {10.3791/59589},
- issn = {1940-087X},
- journal = {JoVE (Journal of Visualized Experiments)},
- keywords = {+Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- number = {146},
- pages = {e59589},
- title = {Mass {Spectrometry}-{Based} {Proteomics} {Analyses} {Using} the {OpenProt} {Database} to {Unveil} {Novel} {Proteins} {Translated} from {Non}-{Canonical} {Open} {Reading} {Frames}},
- url = {https://www.jove.com/video/59589/mass-spectrometry-based-proteomics-analyses-using-openprot-database},
- urldate = {2019-04-24},
- year = {2019}
-}
-
-@article{buhl_prevotella_2020,
- abstract = {A strain of an obligately anaerobic, Gram-­stain-n­ egative rod-­shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879T was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-­length 16S rRNA gene and whole-­genome sequence) revealed the strain to belong to the genus Prevotella, but to be distant from recognized species, with the closest relationship to Prevotella veroralis. Unambiguous identification also proved possible by MALDI-­TOF MS. The genomic DNA G+C content was 41.5 mol\%. Strain A2879T was moderately saccharolytic and proteolytic. The most abundant cellular long-­chain fatty acids were anteiso-C­ 15 : 0 and iso-C­ 15 : 0. In view of these data, strain A2879T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella vespertina sp. nov. is proposed. The type strain is A2879T (=DSM 108027T=CCOS 1233T=CCUG72808T). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.},
- author = {Buhl, Michael and Marschal, Matthias},
- doi = {10.1099/ijsem.0.004316},
- issn = {1466-5026, 1466-5034},
- journal = {International Journal of Systematic and Evolutionary Microbiology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {July},
- title = {Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient},
- url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004316},
- urldate = {2020-08-20},
- year = {2020}
-}
-
-@article{busch_iclip_2019,
- abstract = {Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understanding the complex post-transcriptional regulation of gene expression. This information can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. Here, we present a complete data analysis workflow to reliably detect RBP binding sites from iCLIP data. The workflow covers all steps from the initial quality control of the sequencing reads up to peak calling and quantification of RBP binding. For each tool, we explain the specific requirements for iCLIP data analysis and suggest optimised parameter settings.},
- author = {Busch, Anke and Brüggemann, Mirko and Ebersberger, Stefanie and Zarnack, Kathi},
- doi = {10.1016/j.ymeth.2019.11.008},
- issn = {1046-2023},
- journal = {Methods},
- keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Binding sites, Bioinformatics, Data processing, RNA-binding protein, UV crosslink events, iCLIP},
- language = {en},
- month = {November},
- shorttitle = {{iCLIP} data analysis},
- title = {{iCLIP} data analysis: {A} complete pipeline from sequencing reads to {RBP} binding sites},
- url = {http://www.sciencedirect.com/science/article/pii/S1046202318304948},
- urldate = {2019-11-26},
- year = {2019}
-}
-
-@article{buttimer_isolation_2020,
- author = {Buttimer, Colin and Lynch, Caoimhe and Hendrix, Hanne and Neve, Horst and Noben, Jean-Paul and Lavigne, Rob and Coffey, Aidan},
- doi = {10.3390/antibiotics9060352},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: MDPI AG},
- number = {6},
- pages = {352},
- title = {Isolation and {Characterization} of {Pectobacterium} {Phage} {vB}\_PatM\_CB7: {New} {Insights} into the {Genus} {Certrevirus}},
- url = {https://doi.org/10.3390/antibiotics9060352},
- volume = {9},
- year = {2020}
-}
-
-@article{buttimer_isolation_2020,
- abstract = {To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB\_PatM\_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins\—20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.},
- author = {Buttimer, Colin and Lynch, Caoimhe and Hendrix, Hanne and Neve, Horst and Noben, Jean-Paul and Lavigne, Rob and Coffey, Aidan},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/antibiotics9060352},
- journal = {Antibiotics},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Certrevirus, Pectobacterium atrosepticum, Vequintavirinae, homing endonuclease, phage, phytopathogen, potato blackleg, sigma70 promoter, soft rot disease},
- language = {en},
- month = {June},
- note = {Number: 6
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {6},
- pages = {352},
- shorttitle = {Isolation and {Characterization} of {Pectobacterium} {Phage} {vB}\_PatM\_CB7},
- title = {Isolation and {Characterization} of {Pectobacterium} {Phage} {vB}\_PatM\_CB7: {New} {Insights} into the {Genus} {Certrevirus}},
- url = {https://www.mdpi.com/2079-6382/9/6/352},
- urldate = {2020-08-19},
- volume = {9},
- year = {2020}
-}
-
-@misc{camargo_romera_isoform_2021,
- abstract = {Neuroblastoma (NB) is the most frequent extracranial solid tumour in childhood. The clinical diagnosis of NB is difficult due to the age of the patient and the vague appearance of the symptoms. Moreover, there are two groups of aggressive NBs, one with MYCN amplification and the other with an 11q deletion. Some genes could be a candidate suppressor for NB, e.g., the DLG2 gene that resides within the 11q-deleted region. The DLG2 gene has a large number of exons and multiple isoforms depending on the alternative splicing process. Moreover, these isoforms can include the L27 domain or not. This study aimed to analyse, by applying bioinformatic tools, if isoform 2, which does not have L27 domain, could be a candidate suppressor for this disease. RNA-seq samples from different human cell lines were collected from NCBI and a quality analysis was performed. The filtered samples were run in R and Python programs to do a visualization of the exon expression level and the prediction of Rsubread for exon-exon junctions. The results showed that isoform 2 of DLG2 gene was not expressed in the samples of NB, which is a promising result for being a candidate suppressor of NB. Furthermore, the prediction of exon-exon junctions by Rsubread was confirmed to be very accurate. In conclusion, this study shows that isoform 2 of DLG2 gene could be a candidate tumour suppressor in NB that could, in the future, be used as a target to help to detect earlier the presence of NB and increase the life expectancy of children who suffer from this disease.},
- author = {Camargo Romera, Paula},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Backup Publisher: University of Skövde, School of Bioscience
-Pages: 32},
- publisher = {, School of Bioscience},
- title = {Isoform 2 of {DLG2} gene as a possible candidate tumour suppressor of neuroblastoma},
- year = {2021}
-}
-
-@article{candeliere_draft_2020,
- abstract = {Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes.},
- author = {Candeliere, Francesco and Raimondi, Stefano and Spampinato, Gloria and Tay, Moon Yue Feng and Amaretti, Alberto and Schlundt, Joergen and Rossi, Maddalena},
- copyright = {Copyright © 2020 Candeliere et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.},
- doi = {10.1128/MRA.01247-19},
- issn = {2576-098X},
- journal = {Microbiology Resource Announcements},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {January},
- number = {2},
- pmid = {31919169},
- title = {Draft {Genome} {Sequences} of 12 {Leuconostoc} carnosum {Strains} {Isolated} from {Cooked} {Ham} {Packaged} in a {Modified} {Atmosphere} and from {Fresh} {Sausages}},
- url = {https://mra.asm.org/content/9/2/e01247-19},
- urldate = {2020-01-25},
- volume = {9},
- year = {2020}
-}
-
-@phdthesis{cantarella_insights_2020,
- abstract = {A large portion of the human genome is composed of repeated sequences, with Alu retrotransposons representing the most abundant repetitive elements. Alu sequences belong to the class of the Short Interspersed Nuclear Elements (SINEs) and depend on the Long Interspersed Nuclear Elements (LINEs) for their mobilization into the genome. The efficiency of Alu amplification during primate evolution suggests a positive driving force for their accumulation, bringing up to 1 million copies in the human genome. For unclear reasons, the majority of Alu sequences is repressed by tight epigenetic silencing, which is released in response to cell stresses such as virus infection and cancer progression. Adenovirus 5 (Ad5) is known to cause an increase of Alu transcription in HeLa, myelogenous leukemia and embryonic kidney cell lines, even though the virus factors that are responsible for this transcriptional enhancement have not been identified yet. Potential candidates could be represented by oncovirus proteins that induce a global remodeling of the host epigenetic landscape. For example, the Adenovirus early E1A protein interacts with the host tumor suppressor Rb, the lysine acetylase p300 and the p400 ATP-dependent chromatin remodeling complex, resulting in the induction of quiescent fibroblasts to enter the S-phase of the cell cycle. 
-The exceptional success of Alu expansion and their retention even at the cost of a strong epigenetic silencing, which is released by virus infection, led us to investigate the molecular mechanism of Alus activation and their potential involvement in various cell processes.  
-Firstly, genome-wide Alu profiling was performed in quiescent human primary fibroblasts infected with the Ad5 dl1500 mutant, which only expresses the oncovirus small E1A protein. A total of 1880 Polymerase III (Pol III) transcribed Alus were detected through high throughput RNA-sequencing (RNA-seq), revealing a 4-fold increase of the average Alu expression induced by small E1A.   
-With the aim of identifying small E1A-host protein interactions that are crucial for the activation of Alu expression, the host proteins Rb, p300 and p400 were put under investigation. Alu expression profiling was performed in cells infected with small E1A mutants that are not capable to bind Rb, p300 or p400. RNA-seq and RT-qPCR data revealed that the small E1A-p400 binding mutant was the least efficient in activating Alu expression, whereas a milder effect was reported for small E1A-Rb and small E1A-p300 binding mutants. Moreover, ChIP-sequencing (ChIP-seq) analyses of dl1500 infected fibroblasts revealed an enrichment of H3K4me1 within the body of small E1A-induced Alus. Our data point toward the existence of H3K4me1 Alu loci that are recognized by p400 bound by small E1A, resulting in Alu transcription in response to virus infection. 
-Secondly, two Alu sequences were stably overexpressed in one primary and one cancer cell line (human fibroblasts and HeLa cells, respectively) and differential gene expression in Alu-overexpressing cells was performed through RNA-seq data analysis. Among the two Alu- overexpressing fibroblast cell lines, 330 genes were detected as Differentially Expressed (DE), whereas only two genes were differentially expressed in HeLa cells. Interestingly, DE genes detected in Alu-overexpressing fibroblasts were significantly enriched in pathways belonging to cell cycle progression and mitotic entry. The promotion of cell cycle was also supported by a significantly higher percentage of cells in the S-phase compared to control samples as revealed by flow cytometry.  
-The studies conducted in this work identify Ad5 small E1A as one of the virus factors that enhance Alu transcription, possibly through binding with the p400 complex. Interestingly, the overexpression of two Alu sequences in human fibroblasts leads to the stimulation of cell cycle progression, resulting in the same phenotype as previously observed in Ad5 infected fibroblasts. This brings us to speculate that the overexpression of Alu sequences during stress response to viral infection could be exploited by Ad5 to sustain cell proliferation.},
- author = {Cantarella, Simona},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {Inglese},
- month = {March},
- note = {Accepted: 2020-04-18T06:13:49Z},
- school = {Università degli Studi di Parma. Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale},
- shorttitle = {Insights into {Alu} retrotransposons},
- title = {Insights into {Alu} retrotransposons: mechanism of {Alu} transcriptome alteration in response to virus infection and novel effects on gene expression},
- type = {Doctoral thesis},
- url = {http://dspace-unipr.cineca.it/handle/1889/3997},
- urldate = {2020-05-27},
- year = {2020}
-}
-
-@article{carattoli_evolutionary_2021,
- author = {Carattoli, Alessandra and Arcari, Gabriele and Bibbolino, Giulia and Sacco, Federica and Tomolillo, Dario and Lella, Federica Maria Di and Trancassini, Maria and Faino, Luigi and Venditti, Mario and Antonelli, Guido and Raponi, Giammarco},
- doi = {10.1128/aac.00574-21},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: American Society for Microbiology},
- number = {10},
- title = {Evolutionary {Trajectories} toward {Ceftazidime}-{Avibactam} {Resistance} in {Klebsiella} pneumoniae {Clinical} {Isolates}},
- url = {https://doi.org/10.1128/aac.00574-21},
- volume = {65},
- year = {2021}
-}
-
-@article{cermak_unexpected_2020,
- abstract = {In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.},
- author = {Čermák, Vojtěch and Tyč, Dimitrij and Přibylová, Adéla and Fischer, Lukáš},
- doi = {10.1016/j.bbagrm.2020.194647},
- issn = {1874-9399},
- journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, DNA methylation, PTGS, RNAi, Tobacco BY-2 cell line, dsRNA, siRNA},
- language = {en},
- month = {November},
- number = {11},
- pages = {194647},
- title = {Unexpected variations in posttranscriptional gene silencing induced by differentially produced {dsRNAs} in tobacco cells},
- url = {https://www.sciencedirect.com/science/article/pii/S1874939920302303},
- urldate = {2021-05-15},
- volume = {1863},
- year = {2020}
-}
-
-@article{chen_first_2021,
- author = {Chen, Dong-Bin and Zhang, Ru-Song and Jin, Xiang-Dong and Yang, Jian and Li, Peng and Liu, Yan-Qun},
- doi = {10.1017/s0007485321000808},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Cambridge University Press (CUP)},
- pages = {1--10},
- title = {First complete mitochondrial genome of {Rhodinia} species ({Lepidoptera}: {Saturniidae}): genome description and phylogenetic implication},
- url = {https://doi.org/10.1017/s0007485321000808},
- year = {2021}
-}
-
-@article{chen_versatile_2018,
- abstract = {Abstract.  Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as},
- author = {Chen, Qi and Meng, Xianwen and Liao, Qi and Chen, Ming},
- doi = {10.1093/bib/bby050},
- journal = {Briefings in Bioinformatics},
- keywords = {+RefPublic, {\textgreater}RNA Workbench},
- language = {en},
- month = {June},
- title = {Versatile interactions and bioinformatics analysis of noncoding {RNAs}},
- url = {https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby050/5043119},
- urldate = {2018-07-24},
- year = {2018}
-}
-
-@article{chiara_next_2020,
- author = {Chiara, Matteo and D'Erchia, Anna Maria and Gissi, Carmela and Manzari, Caterina and Parisi, Antonio and Resta, Nicoletta and Zambelli, Federico and Picardi, Ernesto and Pavesi, Giulio and Horner, David S. and Pesole, Graziano},
- doi = {10.1093/bib/bbaa297},
- journal = {Briefings in Bioinformatics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {December},
- note = {Publisher: Oxford University Press (OUP)},
- title = {Next generation sequencing of {SARS}-{CoV}-2 genomes: challenges, applications and opportunities},
- url = {https://doi.org/10.1093/bib/bbaa297},
- year = {2020}
-}
-
-@article{chiara_next_2021,
- abstract = {Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic.Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘vademecum’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.},
- author = {Chiara, Matteo and D’Erchia, Anna Maria and Gissi, Carmela and Manzari, Caterina and Parisi, Antonio and Resta, Nicoletta and Zambelli, Federico and Picardi, Ernesto and Pavesi, Giulio and Horner, David S and Pesole, Graziano},
- doi = {10.1093/bib/bbaa297},
- issn = {1477-4054},
- journal = {Briefings in Bioinformatics},
- keywords = {+RefPublic, +Workbench, {\textgreater}UseGalaxy.eu},
- month = {March},
- number = {2},
- pages = {616--630},
- shorttitle = {Next generation sequencing of {SARS}-{CoV}-2 genomes},
- title = {Next generation sequencing of {SARS}-{CoV}-2 genomes: challenges, applications and opportunities},
- url = {https://doi.org/10.1093/bib/bbaa297},
- urldate = {2021-04-14},
- volume = {22},
- year = {2021}
-}
-
-@article{colin_whats_2022,
- author = {Colin, Luigi and Abed-Navandi, Daniel and Conde, Dalia A. and Craggs, Jamie and Silva, Rita da and Janse, Max and Källström, Björn and Pearce-Kelly, Alexander and Yesson, Chris},
- doi = {10.1007/s12686-021-01250-3},
- journal = {Conservation Genetics Resources},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Springer Science and Business Media LLC},
- title = {What's left in the tank? {Identification} of non-ascribed aquarium's coral collections with {DNA} barcodes as part of an integrated diagnostic approach},
- url = {https://doi.org/10.1007/s12686-021-01250-3},
- year = {2022}
-}
-
-@article{cordellier_next-generation_2021,
- author = {Cordellier, Mathilde and Wojewodzic, Marcin W. and Wessels, Martin and Kuster, Christian and Elert, Eric von},
- doi = {10.1016/j.zool.2021.125895},
- journal = {Zoology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Elsevier BV},
- pages = {125895},
- title = {Next-generation sequencing of {DNA} from resting eggs: signatures of eutrophication in a lake's sediment},
- url = {https://doi.org/10.1016/j.zool.2021.125895},
- year = {2021}
-}
-
-@article{cova_helios_2021,
- author = {Cova, Giovanni and Taroni, Chiara and Deau, Marie-Céline and Cai, Qi and Mittelheisser, Vincent and Philipps, Muriel and Jung, Matthieu and Cerciat, Marie and Gras, Stéphanie Le and Thibault-Carpentier, Christelle and Jost, Bernard and Carlsson, Leif and Thornton, Angela M. and Shevach, Ethan M. and Kirstetter, Peggy and Kastner, Philippe and Chan, Susan},
- doi = {10.1084/jem.20202317},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Rockefeller University Press},
- number = {10},
- title = {Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells},
- url = {https://doi.org/10.1084/jem.20202317},
- volume = {218},
- year = {2021}
-}
-
-@article{dad_molecular_2020,
- abstract = {Recent studies support the assumption that mutation of the X-linked Pig-a gene is most likely responsible for the mutant phenotype of the cells deficient in glycosylphosphatidylinositol (GPI)-anchored proteins quantified in the rodent Pig-a gene mutation assay. In humans, however, mutations in both alleles of one of the 30 other genes involved in GPI-anchor synthesis, e.g., PIG-L and PIG-O, cause reduced expression of surface GPI-anchored proteins. Here, we investigated the possibility that the loss of the GPI-anchor detected by the rat Pig-a assay also could be caused by mutation in other GPI-biosynthesis genes. 31 samples were obtained from 8 inbred and outbred rat strains commonly used for genetic toxicology assays. In order to investigate possible sources of variation in the Pig-a assay, variant DNA sequences were evaluated in Cd59 and 24 GPI-biosynthesis genes. In some genes, such as Pig-n and Pig-u, homozygous variations occurred in all animals, suggesting that these variations are due to deviations in the reference genome. Heterozygous Pig-s, Pig-w, Pig-o, Pig-c, Pgap1, Pgap2, Pig-k and Pig-t variations were found, however, indicating that these genes could serve as targets for mutation in the assay. Protein alignment for these altered genes was conducted with possible human, mouse and rat phenotypic mutants from the literature; this analysis demonstrated that many of the variations that we detected were in non-conserved sequences and that no phenotypes for any of these variants could be inferred from known mutants from the literature. All heterozygous variants were in outbred rats. Overall, the findings of this study cannot totally rule out the possibility that mutations in GPI-biosynthesis genes other than Pig-a are detected in the Pig-a assay, but suggest that if it occurs, it must occur only rarely and therefore mutations in genes other than Pig-a have little impact on rat-based experiments.},
- author = {Dad, Azra and Dobrovolsky, Vasily N. and Heflich, Robert H. and Revollo, Javier R.},
- doi = {10.1016/j.mrgentox.2020.503256},
- issn = {1383-5718},
- journal = {Mutation Research/Genetic Toxicology and Environmental Mutagenesis},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Glycosylphosphatidylinositol anchor, Heterozygous, Homozygous, Inbred, Outbred, Sequence variant},
- language = {en},
- month = {October},
- pages = {503256},
- title = {Molecular analysis of {GPI}-anchor biosynthesis pathway genes in rat strains used for the {Pig}-a gene mutation assay},
- url = {https://www.sciencedirect.com/science/article/pii/S1383571820301261},
- urldate = {2021-04-09},
- volume = {858-860},
- year = {2020}
-}
-
-@article{darkow_small_2021,
- author = {Darkow, Elisa and Nguyen, Thong T. and Stolina, Marina and Kari, Fabian A. and Schmidt, Constanze and Wiedmann, Felix and Baczkó, István and Kohl, Peter and Rajamani, Sridharan and Ravens, Ursula and Peyronnet, Rémi},
- doi = {10.3389/fphys.2021.650964},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Frontiers Media SA},
- title = {Small {Conductance} {Ca2} \${\textbackslash}mathplus\$-{Activated} {K}\${\textbackslash}mathplus\$ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}: {Comparison} {Between} {Donor}, {Atrial} {Fibrillation} and {Heart} {Failure} {Tissue}},
- url = {https://doi.org/10.3389/fphys.2021.650964},
- volume = {12},
- year = {2021}
-}
-
-@article{davey_intrinsically_2019,
- abstract = {Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.},
- author = {Davey, Norman E. and Babu, M. Madan and Blackledge, Martin and Bridge, Alan and Capella-Gutierrez, Salvador and Dosztanyi, Zsuzsanna and Drysdale, Rachel and Edwards, Richard J. and Elofsson, Arne and Felli, Isabella C. and Gibson, Toby J. and Gutmanas, Aleksandras and Hancock, John M. and Harrow, Jen and Higgins, Desmond and Jeffries, Cy M. and Le Mercier, Philippe and Mészáros, Balint and Necci, Marco and Notredame, Cedric and Orchard, Sandra and Ouzounis, Christos A. and Pancsa, Rita and Papaleo, Elena and Pierattelli, Roberta and Piovesan, Damiano and Promponas, Vasilis J. and Ruch, Patrick and Rustici, Gabriella and Romero, Pedro and Sarntivijai, Sirarat and Saunders, Gary and Schuler, Benjamin and Sharan, Malvika and Shields, Denis C. and Sussman, Joel L. and Tedds, Jonathan A. and Tompa, Peter and Turewicz, Michael and Vondrasek, Jiri and Vranken, Wim F. and Wallace, Bonnie Ann and Wichapong, Kanin and Tosatto, Silvio C. E.},
- doi = {10.12688/f1000research.20136.1},
- issn = {2046-1402},
- journal = {F1000Research},
- keywords = {+RefPublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- pages = {1753},
- title = {An intrinsically disordered proteins community for {ELIXIR}},
- url = {https://f1000research.com/articles/8-1753/v1},
- urldate = {2019-11-03},
- volume = {8},
- year = {2019}
-}
-
-@article{delroisse_photophore_2021,
- author = {Delroisse, Jérôme and Duchatelet, Laurent and Flammang, Patrick and Mallefet, Jérôme},
- doi = {10.3389/fmars.2021.627045},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Frontiers Media SA},
- title = {Photophore {Distribution} and {Enzymatic} {Diversity} {Within} the {Photogenic} {Integument} of the {Cookie}-{Cutter} {Shark} {Isistius} brasiliensis ({Chondrichthyes}: {Dalatiidae})},
- url = {https://doi.org/10.3389/fmars.2021.627045},
- volume = {8},
- year = {2021}
-}
-
-@article{deng_gene_2020,
- abstract = {Endothelial cells take pivotal roles in the heart and the vascular system and their differentiation, subspecification and function is determined by gene expression. A stable, in vitro cardiac endothelial cell line could provide high cell numbers as needed for many epigenetic analyses and facilitate the understanding of molecular mechanisms involved in endothelial cell biology. To test their suitability for transcriptomic or epigenetic studies, we compared the transcriptome of cultured immortalized mouse cardiac endothelial cells (MCEC) to primary cardiac endothelial cells (pEC). Whole transcriptome comparison of MCEC and pEC showed a correlation of 0.75–0.77. Interestingly, correlation of gene expression declined in endothelial cell-typical genes. In MCEC, we found a broad downregulation of genes that are highly expressed in pEC, including well-described markers of endothelial cell differentiation. Accordingly, systematic analysis revealed a downregulation of genes associated with typical endothelial cell functions in MCEC, while genes related to mitotic cell cycle were upregulated when compared to pEC. In conclusion, the findings from this study suggest that primary cardiac endothelial cells should preferably be used for genome-wide transcriptome or epigenome studies. The suitability of in vitro cell lines for experiments investigating single genes or signaling pathways should be carefully validated before use.},
- author = {Deng, Lisa and Pollmeier, Luisa and Zhou, Qian and Bergemann, Stella and Bode, Christoph and Hein, Lutz and Lother, Achim},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-59213-x},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {1--9},
- title = {Gene expression in immortalized versus primary isolated cardiac endothelial cells},
- url = {https://www.nature.com/articles/s41598-020-59213-x},
- urldate = {2020-03-02},
- volume = {10},
- year = {2020}
-}
-
-@article{deng_lamp_2022,
- author = {Deng, Sheng and Ma, Xin and Chen, Yifan and Feng, Hui and Zhou, Dongmei and Wang, Xiaoyu and Zhang, Yong and Zhao, Min and Zhang, Jinfeng and Daly, Paul and Wei, Lihui},
- doi = {10.1094/pdis-06-21-1223-re},
- journal = {Plant Disease},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Scientific Societies},
- number = {1},
- pages = {231--246},
- title = {{LAMP} {Assay} for {Distinguishing} {Fusarium} oxysporum and {Fusarium} commune in {Lotus} ({Nelumbo} nucifera) {Rhizomes}},
- url = {https://doi.org/10.1094/pdis-06-21-1223-re},
- volume = {106},
- year = {2022}
-}
-
-@article{dhamija_pan-cancer_2020,
- abstract = {Nonstop or stop-loss mutations convert a stop into a sense codon, resulting in translation into the 3′ untranslated region as a nonstop extension mutation to the next in-frame stop codon or as a readthrough mutation into the poly-A tail. Nonstop mutations have been characterized in hereditary diseases, but not in cancer genetics. In a pan-cancer analysis, we curated and analysed 3,412 nonstop mutations from 62 tumour entities, generating a comprehensive database at http://NonStopDB.dkfz.de. Six different nonstop extension mutations affected the tumour suppressor SMAD4, extending its carboxy terminus by 40 amino acids. These caused rapid degradation of the SMAD4 mutants via the ubiquitin–proteasome system. A hydrophobic degron signal sequence of ten amino acids within the carboxy-terminal extension was required to induce complete loss of the SMAD4 protein. Thus, we discovered that nonstop mutations can be functionally important in cancer and characterize their loss-of-function impact on the tumour suppressor SMAD4.},
- author = {Dhamija, Sonam and Yang, Chul Min and Seiler, Jeanette and Myacheva, Ksenia and Caudron-Herger, Maiwen and Wieland, Angela and Abdelkarim, Mahmoud and Sharma, Yogita and Riester, Marisa and Groß, Matthias and Maurer, Jochen and Diederichs, Sven},
- copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
- doi = {10.1038/s41556-020-0551-7},
- issn = {1476-4679},
- journal = {Nature Cell Biology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- note = {Number: 8
-Publisher: Nature Publishing Group},
- number = {8},
- pages = {999--1010},
- title = {A pan-cancer analysis reveals nonstop extension mutations causing {SMAD4} tumour suppressor degradation},
- url = {https://www.nature.com/articles/s41556-020-0551-7},
- urldate = {2020-08-12},
- volume = {22},
- year = {2020}
-}
-
-@article{di_dalmazi_dna_2020,
- abstract = {DNA methylation has been identified among putative regulatory mechanisms for CYP11B2 expression in primary aldosteronism.The objective of this work is to investigate DNA methylation and expression of genes encoding steroidogenic enzymes in benign adrenocortical tumors.This cross-sectional study took place at university hospitals.We collected fresh-frozen tissues from patients with benign adrenocortical adenomas (n = 48) (nonfunctioning n = 9, autonomous cortisol secretion n = 9, Cushing syndrome n = 17, aldosterone-producing [APA] n = 13) and adrenal cortex adjacent to APA (n = 12). We collected formalin-fixed, paraffin-embedded (FFPE) specimens of paired APA and concurrent aldosterone-producing cell clusters (APCCs) (n = 6).DNA methylation levels were evaluated by quantitative bisulfite next-generation sequencing in fresh-frozen tissues (CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD3B1, HSD3B2, NR5A1, STAR, and TSPO) and FFPE APA/APCC paired samples (CYP11B2). CYP11B1, CYP11B2, CYP17, CYP21, and STAR gene expressions were examined by quantitative real-time polymerase chain reaction.The main outcome measure was DNA methylation.CYP11B2 methylation levels were significantly lower in APA than in other adrenal tissues (P \< .001). Methylation levels of the remaining genes were comparable among groups. Overall, CYP11B2 expression and DNA methylation were negatively correlated (ρ = –0.379; P = .003). In FFPE-paired APA/APCC samples, CYP11B2 methylation level was significantly lower in APA than in concurrent APCCs (P = .028).DNA methylation plays a regulatory role for CYP11B2 expression and may contribute to aldosterone hypersecretion in APA. Lower CYP11B2 methylation levels in APA than in APCCs may suggest an APCC-to-APA switch via progressive CYP11B2 demethylation. Conversely, DNA methylation seems not to be relevant in regulating the expression of genes encoding steroidogenic enzymes other than CYP11B2.},
- author = {Di Dalmazi, Guido and Morandi, Luca and Rubin, Beatrice and Pilon, Catia and Asioli, Sofia and Vicennati, Valentina and De Leo, Antonio and Ambrosi, Francesca and Santini, Donatella and Pagotto, Uberto and Maffeis, Valeria and Fassina, Ambrogio and Fallo, Francesco},
- doi = {10.1210/clinem/dgaa585},
- issn = {0021-972X},
- journal = {The Journal of Clinical Endocrinology \& Metabolism},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {December},
- number = {12},
- pages = {e4605--e4615},
- shorttitle = {{DNA} {Methylation} of {Steroidogenic} {Enzymes} in {Benign} {Adrenocortical} {Tumors}},
- title = {{DNA} {Methylation} of {Steroidogenic} {Enzymes} in {Benign} {Adrenocortical} {Tumors}: {New} {Insights} in {Aldosterone}-{Producing} {Adenomas}},
- url = {https://doi.org/10.1210/clinem/dgaa585},
- urldate = {2021-02-08},
- volume = {105},
- year = {2020}
-}
-
-@article{dias_pathogenicity_2022,
- author = {Dias, Diana and Costa, Sávio and Fonseca, Carlos and Baraúna, Rafael and Caetano, Tânia and Mendo, Sónia},
- doi = {10.1016/j.scitotenv.2021.152324},
- journal = {Science of The Total Environment},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Elsevier BV},
- pages = {152324},
- title = {Pathogenicity of {Shiga} toxin-producing {Escherichia} coli ({STEC}) from wildlife: {Should} we care?},
- url = {https://doi.org/10.1016/j.scitotenv.2021.152324},
- volume = {812},
- year = {2022}
-}
-
-@article{dorn_linc00261_2020,
- abstract = {Pancreatic adenocarcinoma (PDAC) is one of the major causes of cancer-associated deaths worldwide, with a dismal prognosis that has not significantly changed over the last decades. Transcriptional analysis has provided valuable insights into pancreatic tumorigenesis. Specifically, pancreatic cancer subtypes were identified, characterized by specific mutations and gene expression changes associated with differences in patient survival. In addition to differentially regulated mRNAs, non-coding RNAs, including long non-coding RNAs (lncRNAs), were shown to have subtype-specific expression patterns. Hence, we aimed to characterize prognostic lncRNAs with deregulated expression in the squamous subtype of PDAC, which has the worst prognosis. Extensive in silico analyses followed by in vitro experiments identified long intergenic non-coding RNA 261 (LINC00261) as a downregulated lncRNA in the squamous subtype of PDAC, which is generally associated with transforming growth factor \β (TGF\β) signaling in human cancer cells. Its genomic neighbor, the transcription factor forkhead box protein A2 (FOXA2), regulated LINC00261 expression by direct binding of the LINC00261 promoter. CRISPR-mediated knockdown and promoter knockout validated the importance of LINC00261 in TGF\β-mediated epithelial\–mesenchymal transition (EMT) and established the epithelial marker E-cadherin, an important cell adhesion protein, as a downstream target of LINC00261. Consequently, depletion of LINC00261 enhanced motility and invasiveness of PANC-1 cells in vitro. Altogether, our data suggest that LINC00261 is an important tumor-suppressive lncRNA in PDAC that is involved in maintaining a pro-epithelial state associated with favorable disease outcome.},
- author = {Dorn, Agnes and Glaß, Markus and Neu, Carolin T. and Heydel, Beate and Hüttelmaier, Stefan and Gutschner, Tony and Haemmerle, Monika},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/cancers12051227},
- journal = {Cancers},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, CDH1, EMT, FOXA2, LINC00261, PDAC, TGFβ, lncRNA},
- language = {en},
- month = {May},
- note = {Number: 5
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {5},
- pages = {1227},
- title = {{LINC00261} {Is} {Differentially} {Expressed} in {Pancreatic} {Cancer} {Subtypes} and {Regulates} a {Pro}-{Epithelial} {Cell} {Identity}},
- url = {https://www.mdpi.com/2072-6694/12/5/1227},
- urldate = {2020-05-27},
- volume = {12},
- year = {2020}
-}
-
-@article{dorone_prion-like_2021,
- abstract = {Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.},
- author = {Dorone, Yanniv and Boeynaems, Steven and Flores, Eduardo and Jin, Benjamin and Hateley, Shannon and Bossi, Flavia and Lazarus, Elena and Pennington, Janice G. and Michiels, Emiel and De Decker, Mathias and Vints, Katlijn and Baatsen, Pieter and Bassel, George W. and Otegui, Marisa S. and Holehouse, Alex S. and Exposito-Alonso, Moises and Sukenik, Shahar and Gitler, Aaron D. and Rhee, Seung Y.},
- doi = {10.1016/j.cell.2021.06.009},
- issn = {0092-8674},
- journal = {Cell},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, adaptation, bet hedging, biomolecular condensate, intrinsically disordered proteins, phase separation, prion-like, salt stress, seed germination, water sensing, water stress},
- language = {en},
- month = {August},
- number = {16},
- pages = {4284--4298.e27},
- title = {A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation},
- url = {https://www.sciencedirect.com/science/article/pii/S0092867421007108},
- urldate = {2021-08-24},
- volume = {184},
- year = {2021}
-}
-
-@article{dugar_chromosomal_2022,
- author = {Dugar, Gaurav and Hofmann, Andreas and Heermann, Dieter W and Hamoen, Leendert W},
- journal = {Nature Genetics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Nature Publishing Group},
- pages = {1--8},
- title = {A chromosomal loop anchor mediates bacterial genome organization},
- year = {2022}
-}
-
-@article{dvir_uncovering_2021,
- author = {Dvir, Shlomi and Argoetti, Amir and Lesnik, Chen and Roytblat, Mark and Shriki, Kohava and Amit, Michal and Hashimshony, Tamar and Mandel-Gutfreund, Yael},
- doi = {10.1016/j.celrep.2021.109198},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: Elsevier BV},
- number = {9},
- pages = {109198},
- title = {Uncovering the {RNA}-binding protein landscape in the pluripotency network of human embryonic stem cells},
- url = {https://doi.org/10.1016/j.celrep.2021.109198},
- volume = {35},
- year = {2021}
-}
-
-@article{eggenhofer_cmv_2018,
- abstract = {SummaryA standard method for the identification of novel RNAs or proteins is homology search via probabilistic models. One approach relies on the definition of families, which can be encoded as covariance models (CMs) or Hidden Markov Models (HMMs). While being powerful tools, their complexity makes it tedious to investigate them in their (default) tabulated form. This specifically applies to the interpretation of comparisons between multiple models as in family clans. The Covariance model visualization tools (CMV) visualize CMs or HMMs to: I) Obtain an easily interpretable representation of HMMs and CMs; II) Put them in context with the structural sequence alignments they have been created from; III) Investigate results of model comparisons and highlight regions of interest.AvailabilitySource code (http://www.github.com/eggzilla/cmv), web-service (http://rna.informatik.uni-freiburg.de/CMVS) Contactegg@informatik.uni-freiburg.de, choener@bioinf.uni-leipzig.deSupplementary informationSupplementary data available online.},
- author = {Eggenhofer, Florian and Hofacker, Ivo L. and Backofen, Rolf and Höner zu Siederdissen, Christian and Valencia, Alfonso},
- doi = {10.1093/bioinformatics/bty158},
- journal = {Bioinformatics},
- keywords = {+RefPublic, {\textgreater}RNA Workbench},
- language = {en},
- month = {March},
- title = {{CMV} - {Visualization} for {RNA} and {Protein} family models and their comparisons},
- url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty158/4938485},
- urldate = {2018-03-23},
- year = {2018}
-}
-
-@article{emperle_mutations_2019,
- abstract = {Abstract.  Somatic DNMT3A mutations at R882 are frequently observed in AML patients including the very abundant R882H, but also R882C, R882P and R882S. Using de},
- author = {Emperle, Max and Adam, Sabrina and Kunert, Stefan and Dukatz, Michael and Baude, Annika and Plass, Christoph and Rathert, Philipp and Bashtrykov, Pavel and Jeltsch, Albert},
- doi = {10.1093/nar/gkz911},
- journal = {Nucleic Acids Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- title = {Mutations of {R882} change flanking sequence preferences of the {DNA} methyltransferase {DNMT3A} and cellular methylation patterns},
- url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz911/5588689},
- urldate = {2019-11-06},
- year = {2019}
-}
-
-@article{espenshade_influence_2019,
- abstract = {The aerial surfaces of plants harbour diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterised the epiphytic microbial communities on leaves of Platanus x hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city centre compared to the natural site, and also more human-associated genera were found colonising the leaves from the city centre. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.},
- author = {Espenshade, Jordan and Thijs, Sofie and Gawronski, Stanislaw and Bové, Hannelore and Weyens, Nele and Vangronsveld, Jaco},
- doi = {10.3389/fmicb.2019.00675},
- issn = {1664-302X},
- journal = {Frontiers in Microbiology},
- keywords = {+Methods, +UsePublic, {\textgreater}Huttenhower, {\textgreater}UseGalaxy.eu, Biodiversity, Particulate Matter, Phyllosphere bacteria, Plant-microbe association, black carbon, phylloremediation, urban microbiome},
- language = {English},
- title = {Influence of {Urbanization} on {Epiphytic} {Bacterial} {Communities} of the {Platanus} × hispanica {Tree} {Leaves} in a {Biennial} {Study}},
- url = {https://www.frontiersin.org/articles/10.3389/fmicb.2019.00675/full},
- urldate = {2019-04-23},
- volume = {10},
- year = {2019}
-}
-
-@article{espindola-hernandez_genomic_2020,
- abstract = {Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.},
- author = {Espíndola-Hernández, Pamela and Mueller, Jakob C and Carrete, Martina and Boerno, Stefan and Kempenaers, Bart},
- doi = {10.1093/gbe/evaa166},
- editor = {Mank, Judith},
- issn = {1759-6653},
- journal = {Genome Biology and Evolution},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- number = {10},
- pages = {1895--1908},
- title = {Genomic {Evidence} for {Sensorial} {Adaptations} to a {Nocturnal} {Predatory} {Lifestyle} in {Owls}},
- url = {https://academic.oup.com/gbe/article/12/10/1895/5889951},
- urldate = {2021-08-24},
- volume = {12},
- year = {2020}
-}
-
-@article{estell_zc3h4_2021,
- author = {Estell, Chris and Davidson, Lee and Steketee, Pieter C. and Monier, Adam and West, Steven},
- doi = {10.7554/elife.67305},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: eLife Sciences Publications, Ltd},
- title = {{ZC3H4} restricts non-coding transcription in human cells},
- url = {https://doi.org/10.7554/elife.67305},
- volume = {10},
- year = {2021}
-}
-
-@article{estrada_mallarino_nephronophthisis_2020,
- abstract = {Mutations of cilia-associated molecules cause multiple developmental defects that are collectively termed ciliopathies. However, several ciliary proteins, involved in gating access to the cilium, also assume localizations at other cellular sites including the nucleus, where they participate in DNA damage responses to maintain tissue integrity. Molecular insight into how these molecules execute such diverse functions remains limited. A mass spectrometry screen for ANKS6-interacting proteins suggested an involvement of ANKS6 in RNA processing and/or binding. Comparing the RNA-binding properties of the known RNA-binding protein BICC1 with the three ankyrin-repeat proteins ANKS3, ANKS6 (NPHP16) and INVERSIN (NPHP2) confirmed that certain nephronophthisis (NPH) family members can interact with RNA molecules. We also observed that BICC1 and INVERSIN associate with stress granules in response to translational inhibition. Furthermore, BICC1 recruits ANKS3 and ANKS6 into TIA-1-positive stress granules after exposure to hippuristanol. Our findings uncover a novel function of NPH family members, and provide further evidence that NPH family members together with BICC1 are involved in stress responses to maintain tissue and organ integrity.},
- author = {Estrada Mallarino, Luisa and Engel, Christina and Ilık, İbrahim Avşar and Maticzka, Daniel and Heyl, Florian and Müller, Barbara and Yakulov, Toma A. and Dengjel, Jörn and Backofen, Rolf and Akhtar, Asifa and Walz, Gerd},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-72905-8},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}RNA Workbench},
- language = {en},
- month = {September},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {15954},
- title = {Nephronophthisis gene products display {RNA}-binding properties and are recruited to stress granules},
- url = {https://www.nature.com/articles/s41598-020-72905-8},
- urldate = {2021-04-14},
- volume = {10},
- year = {2020}
-}
-
-@article{etherington_galaxy-based_2019,
- abstract = {AbstractBackground.  It is not a trivial step to move from single-cell RNA-sequencing (scRNA-seq) data production to data analysis. There is a lack of intuitive},
- author = {Etherington, Graham J. and Soranzo, Nicola and Mohammed, Suhaib and Haerty, Wilfried and Davey, Robert P. and Palma, Federica Di},
- doi = {10.1093/gigascience/giz144},
- journal = {GigaScience},
- keywords = {+Education, +Galactic, +RefPublic, +Tools, {\textgreater}SingleCell, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- number = {12},
- title = {A {Galaxy}-based training resource for single-cell {RNA}-sequencing quality control and analyses},
- url = {https://academic.oup.com/gigascience/article/8/12/giz144/5673460},
- urldate = {2019-12-21},
- volume = {8},
- year = {2019}
-}
-
-@article{faddetta_endophytic_2021,
- author = {Faddetta, Teresa and Abbate, Loredana and Alibrandi, Pasquale and Arancio, Walter and Siino, Davide and Strati, Francesco and Filippo, Carlotta De and Bosco, Sergio Fatta Del and Carimi, Francesco and Puglia, Anna Maria and Cardinale, Massimiliano and Gallo, Giuseppe and Mercati, Francesco},
- doi = {10.1038/s41598-021-86399-5},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {The endophytic microbiota of {Citrus} limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures},
- url = {https://doi.org/10.1038/s41598-021-86399-5},
- volume = {11},
- year = {2021}
-}
-
-@article{fahrner_democratizing_2022,
- author = {Fahrner, Matthias and Föll, Melanie Christine and Grüning, Björn Andreas and Bernt, Matthias and Röst, Hannes and Schilling, Oliver},
- doi = {10.1093/gigascience/giac005},
- journal = {GigaScience},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Oxford University Press (OUP)},
- title = {Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the {Galaxy} framework},
- url = {https://doi.org/10.1093/gigascience/giac005},
- volume = {11},
- year = {2022}
-}
-
-@article{fahrner_systematic_2021,
- abstract = {Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventional settings, such as fully specific enzymatic constraints. Here we evaluated the impact of the fragment mass tolerance in combination with the enzymatic constraints on the performance of three search engines. Three open-source search engines (Myrimatch, X! Tandem, and MSGF+) were evaluated concerning the suitability in semi- and unspecific searches as well as the importance of accurate fragment mass spectra in non-specific peptide searches. We then performed a semispecific reanalysis of the published NCI-60 deep proteome data applying the most suited parameters. Semi- and unspecific LC-MS/MS data analyses particularly benefit from accurate fragment mass spectra while this effect is less pronounced for conventional, fully specific peptide-spectrum matching. Search speed differed notably between the three search engines for semi- and non-specific peptide-spectrum matching. Semispecific reanalysis of NCI-60 proteome data revealed hundreds of previously undescribed N-terminal peptides, including cases of proteolytic processing or likely alternative translation start sites, some of which were ubiquitously present in all cell lines of the reanalyzed panel. Highly accurate MS2 fragment data in combination with modern open-source search algorithms enable the confident identification of semispecific peptides from large proteomic datasets. The identification of previously undescribed N-terminal peptides in published studies highlights the potential of future reanalysis and data mining in proteomic datasets.},
- author = {Fahrner, Matthias and Kook, Lucas and Fröhlich, Klemens and Biniossek, Martin L. and Schilling, Oliver},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/proteomes9020026},
- journal = {Proteomes},
- keywords = {+Methods, +Shared, +Stellar, +UsePublic, {\textgreater}UseGalaxy.eu, NCI-60 reanalysis, endogenous proteolysis, fragment mass tolerance, mass spectrometry, semispecific peptide search},
- language = {en},
- month = {June},
- note = {Number: 2
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {2},
- pages = {26},
- title = {A {Systematic} {Evaluation} of {Semispecific} {Peptide} {Search} {Parameter} {Enables} {Identification} of {Previously} {Undescribed} {N}-{Terminal} {Peptides} and {Conserved} {Proteolytic} {Processing} in {Cancer} {Cell} {Lines}},
- url = {https://www.mdpi.com/2227-7382/9/2/26},
- urldate = {2021-05-27},
- volume = {9},
- year = {2021}
-}
-
-@article{fallmann_rna_2019,
- abstract = {Abstract.  RNA has become one of the major research topics in molecular biology. As a central player in key processes regulating gene expression, RNA is in the},
- author = {Fallmann, Jörg and Videm, Pavankumar and Bagnacani, Andrea and Batut, Bérénice and Doyle, Maria A. and Klingstrom, Tomas and Eggenhofer, Florian and Stadler, Peter F. and Backofen, Rolf and Grüning, Björn},
- doi = {10.1093/nar/gkz353},
- journal = {Nucleic Acids Research},
- keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}RNA Workbench},
- language = {en},
- month = {May},
- shorttitle = {The {RNA} workbench 2.0},
- title = {The {RNA} workbench 2.0: next generation {RNA} data analysis},
- url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz353/5487675},
- urldate = {2019-05-26},
- year = {2019}
-}
-
-@article{farmiloe_widespread_2020,
- abstract = {The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome.This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.},
- author = {Farmiloe, Grace and Lodewijk, Gerrald A. and Robben, Stijn F. and van Bree, Elisabeth J. and Jacobs, Frank M. J.},
- doi = {10.1098/rstb.2019.0333},
- journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org},
- month = {March},
- note = {Publisher: Royal Society},
- number = {1795},
- pages = {20190333},
- title = {Widespread correlation of {KRAB} zinc finger protein binding with brain-developmental gene expression patterns},
- url = {https://royalsocietypublishing.org/doi/full/10.1098/rstb.2019.0333},
- urldate = {2020-03-05},
- volume = {375},
- year = {2020}
-}
-
-@article{feldker_genome-wide_2020,
- abstract = {Abstract Invasion, metastasis and therapy resistance are the major cause of cancer-associated deaths, and the EMT-inducing transcription factor ZEB1 is a crucial stimulator of these processes. While work on ZEB1 has mainly focused on its role as a transcriptional repressor, it can also act as a transcriptional activator. To further understand these two modes of action, we performed a genome-wide ZEB1 binding study in triple-negative breast cancer cells. We identified ZEB1 as a novel interactor of the AP-1 factors FOSL1 and JUN and show that, together with the Hippo pathway effector YAP, they form a transactivation complex, predominantly activating tumour-promoting genes, thereby synergising with its function as a repressor of epithelial genes. High expression of ZEB1, YAP, FOSL1 and JUN marks the aggressive claudin-low subtype of breast cancer, indicating the translational relevance of our findings. Thus, our results link critical tumour-promoting transcription factors: ZEB1, AP-1 and Hippo pathway factors. Disturbing their molecular interaction may provide a promising treatment option for aggressive cancer types.},
- author = {Feldker, Nora and Ferrazzi, Fulvia and Schuhwerk, Harald and Widholz, Sebastian A and Guenther, Kerstin and Frisch, Isabell and Jakob, Kathrin and Kleemann, Julia and Riegel, Dania and Bönisch, Ulrike and Lukassen, Sören and Eccles, Rebecca L and Schmidl, Christian and Stemmler, Marc P and Brabletz, Thomas and Brabletz, Simone},
- doi = {10.15252/embj.2019103209},
- issn = {0261-4189},
- journal = {The EMBO Journal},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, AP-1, ZEB1, breast cancer, epithelial to mesenchymal transition},
- month = {July},
- note = {Publisher: John Wiley \& Sons, Ltd},
- number = {n/a},
- pages = {e103209},
- title = {Genome-wide cooperation of {EMT} transcription factor {ZEB1} with {YAP} and {AP}-1 in breast cancer},
- url = {https://www.embopress.org/doi/10.15252/embj.2019103209},
- urldate = {2020-08-18},
- volume = {n/a},
- year = {2020}
-}
-
-@article{fell_fibcd1_2021,
- author = {Fell, Christopher W. and Hagelkruys, Astrid and Cicvaric, Ana and Horrer, Marion and Liu, Lucy and Li, Joshua Shing Shun and Stadlmann, Johannes and Polyansky, Anton A. and Mereiter, Stefan and Tejada, Miguel Angel and Kokotović, Tomislav and Scaramuzza, Angelica and Twyman, Kimberly A. and Morrow, Michelle M. and Juusola, Jane and Yan, Huifang and Wang, Jingmin and Burmeister, Margit and Andersen, Thomas Levin and Wirnsberger, Gerald and Holmskov, Uffe and Perrimon, Norbert and Zagrović, Bojan and Monje, Francisco J. and Moeller, Jesper Bonnet and Penninger, Josef M. and Nagy, Vanja},
- doi = {10.1101/2021.09.09.459581},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {{FIBCD1} is a {Conserved} {Receptor} for {Chondroitin} {Sulphate} {Proteoglycans} of the {Brain} {Extracellular} {Matrix} and a {Candidate} {Gene} for a {Complex} {Neurodevelopmental} {Disorder}},
- url = {https://doi.org/10.1101/2021.09.09.459581},
- year = {2021}
-}
-
-@article{feng_scarless_2021,
- author = {Feng, Siqian and Lu, Shan and Grueber, Wesley B. and Mann, Richard S.},
- doi = {10.1093/genetics/iyab012},
- editor = {Rong, Y. S.},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Oxford University Press (OUP)},
- number = {3},
- title = {Scarless engineering of the {Drosophila} genome near any site-specific integration site},
- url = {https://doi.org/10.1093/genetics/iyab012},
- volume = {217},
- year = {2021}
-}
-
-@phdthesis{fernandes_guavadb_2020,
- author = {Fernandes, Miquéias},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {pt},
- school = {Universidade Federal do Espírito Santo},
- title = {{GuavaDB}: {O} {BANCO} {DE} {DADOS} {DA} {GENÔMICA} {DE} {Psidium} guajava {L}.},
- url = {http://portais4.ufes.br/posgrad/teses/tese_14035_Disserta%E7%E3o%20Final%20Miqu%E9ias%20Fernandes.pdf},
- year = {2020}
-}
-
-@article{fiedler_taxonomic_2021,
- author = {Fiedler, Gregor and Herbstmann, Anna-Delia and Doll, Etienne and Wenning, Mareike and Brinks, Erik and Kabisch, Jan and Breitenwieser, Franziska and Lappann, Martin and Böhnlein, Christina and Franz, Charles M. A. P.},
- doi = {10.3390/microorganisms9020246},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: MDPI AG},
- number = {2},
- pages = {246},
- title = {Taxonomic {Evaluation} of the {Heyndrickxia} ({Basonym} {Bacillus}) sporothermodurans {Group} ({H}. sporothermodurans, {H}. vini, {H}. oleronia) {Based} on {Whole} {Genome} {Sequences}},
- url = {https://doi.org/10.3390/microorganisms9020246},
- volume = {9},
- year = {2021}
-}
-
-@article{foll_accessible_2019,
- abstract = {AbstractBackground.  Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial},
- author = {Föll, Melanie Christine and Moritz, Lennart and Wollmann, Thomas and Stillger, Maren Nicole and Vockert, Niklas and Werner, Martin and Bronsert, Peter and Rohr, Karl and Grüning, Björn Andreas and Schilling, Oliver},
- doi = {10.1093/gigascience/giz143},
- journal = {GigaScience},
- keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, {\textgreater}Galaxy-P, {\textgreater}MSI, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, {\textgreater}Workflow4Metabolomics},
- language = {en},
- month = {December},
- number = {12},
- title = {Accessible and reproducible mass spectrometry imaging data analysis in {Galaxy}},
- url = {https://academic.oup.com/gigascience/article/8/12/giz143/5670614},
- urldate = {2020-01-06},
- volume = {8},
- year = {2019}
-}
-
-@article{foll_moving_2021,
- abstract = {Background Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens. This allows for spatial characterization of molecular compositions of different tissue types and tumor subtypes, which bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of an urothelial carcinoma dataset.
-Methods Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle invasive urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list.
-Results Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle invasive tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: Stromal tissue was characterized by collagen type I peptides and tumor tissue by histone and heat shock protein beta-1 peptides.Intermediate filaments such as cytokeratins and vimentin were discriminative between the tumors with different muscle-infiltration status. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder\_MSI\_Manuscript\_Galaxy\_links.
-Conclusion Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.},
- author = {Föll, Melanie Christine and Volkmann, Veronika and Enderle-Ammour, Kathrin and Wilhelm, Konrad and Guo, Dan and Vitek, Olga and Bronsert, Peter and Schilling, Oliver},
- copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
- doi = {10.1101/2021.08.09.455649},
- journal = {bioRxiv},
- keywords = {+Galactic, +IsGalaxy, +Methods, +Reproducibility, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- note = {Company: Cold Spring Harbor Laboratory
-Distributor: Cold Spring Harbor Laboratory
-Label: Cold Spring Harbor Laboratory
-Section: New Results
-Type: article},
- pages = {2021.08.09.455649},
- shorttitle = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses},
- title = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: {A} case study of an urothelial cancer cohort analyzed in the {Galaxy} framework},
- url = {https://doi.org/10.1101/2021.08.09.455649},
- urldate = {2021-09-15},
- year = {2021}
-}
-
-@article{forth_highly_2019,
- abstract = {Library preparation is a crucial step in next-generation sequencing workflows. Key determinants of successful library preparation are the available amount of input DNA and the efficiency of the conversion of this DNA into functional library molecules. While the standard blunt-end ligation protocol for Ion Torrent libraries has a theoretical maximum efficiency of 25\%, Y-adapters enable highly efficient library preparation by (i) sticky-end ligation and (ii) rendering both DNA strands functional for sequencing, hence resulting in a theoretical efficiency of up to 100\%. Moreover, the generation of adapter dimers is reduced. Therefore, we designed, optimized and validated Y-adapters compatible with Ion Torrent sequencing. These facilitate higher library yields combined with overall high sequencing performance regarding the key characteristics read-length, base quality, and library complexity.},
- author = {Forth, Leonie F and Höper, Dirk},
- doi = {10.2144/btn-2019-0035},
- issn = {0736-6205},
- journal = {BioTechniques},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {October},
- title = {Highly efficient library preparation for {Ion} {Torrent} sequencing using {Y}-adapters},
- url = {https://www.future-science.com/doi/10.2144/btn-2019-0035},
- urldate = {2019-11-05},
- year = {2019}
-}
-
-@article{foschini_methylation_2020,
- abstract = {Background: Androgen Receptor (AR) has been described to play a prominent role in Male Breast Cancer (MBC). It maps on chromosome X, and recent reports indicate that X chromosome polysomy is frequent in MBC. Since the response to anti-androgen therapy may depend on AR polysomy and on its overexpression similarly to prostate cancer, aim of the present study was to investigate the DNA methylation level of AR and its coregulators, especially those mapped on the X chromosome, that may influence the activity of AR in MBC. Methods: The DNA methylation level of AR, MAGEA2, MAGEA11, MAGEC1, MAGEC2, FLNA, HDAC6, and UXT, mapped on the X chromosome, was evaluated by quantitative Bisulfite-NGS. Bioinformatic analysis was performed in a GalaxyProject environment using BWA-METH, MethylDackel, and Methylation Plotter tools. The study population consisted of MBC (41 cases) compared with gynecomastia (15 cases). Results: MAGEA family members, especially MAGEA2, MAGEA11, MAGEC, and UXT and HDAC6 showed hypomethylation of several CpGs, reaching statistical significance by the Kruskal-Wallis test (p{\textless}0.01) in MBC when compared to gynecomastia. AR showed almost no methylation at all. Conclusions: Our study demonstrated for the first time that MAGEA family members mapped on X chromosome and coregulators of AR, are hypomethylated in male IDC. This may lead to their overexpression, enhancing AR activity, while AR itself shows very little methylation.},
- author = {Foschini, Maria P. and Morandi, Luca and Sanchez, Alejandro M. and Santoro, Angela and Mulè, Antonino and Zannoni, Gian Franco and Varga, Zsuzsanna and Moskovszky, Linda and Cucchi, Maria C. and Moelans, Cathy B. and Giove, Gianluca and van Diest, Paul J. and Masetti, Riccardo},
- doi = {10.3389/fonc.2020.00784},
- issn = {2234-943X},
- journal = {Frontiers in Oncology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, BWA, DNA Methylation, FLNA, HDAC6, MAGE family, UXT, X-chromosome, androgen receptor, male breast cancer},
- language = {English},
- note = {Publisher: Frontiers},
- title = {Methylation {Profile} of {X}-{Chromosome}–{Related} {Genes} in {Male} {Breast} {Cancer}},
- url = {https://www.frontiersin.org/articles/10.3389/fonc.2020.00784/full},
- urldate = {2020-08-19},
- volume = {10},
- year = {2020}
-}
-
-@article{friedrich_identification_2021,
- author = {Friedrich, Sebastian and Müller, Hannah and Riesterer, Caroline and Schüller, Hannah and Friedrich, Katja and Wörner, Carlotta Leonie and Busch, Tilman and Viau, Amandine and Kuehn, E. Wolfgang and Köttgen, Michael and Hofherr, Alexis},
- doi = {10.1038/s41598-021-94442-8},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia},
- url = {https://doi.org/10.1038/s41598-021-94442-8},
- volume = {11},
- year = {2021}
-}
-
-@article{friedrich_tryptophan_2021,
- abstract = {The dynamics and phenotypes of intratumoral myeloid cells during tumor progression are poorly understood. Here we define myeloid cellular states in gliomas by longitudinal single-cell profiling and demonstrate their strict control by the tumor genotype: in isocitrate dehydrogenase (IDH)-mutant tumors, differentiation of infiltrating myeloid cells is blocked, resulting in an immature phenotype. In late-stage gliomas, monocyte-derived macrophages drive tolerogenic alignment of the microenvironment, thus preventing T cell response. We define the IDH-dependent tumor education of infiltrating macrophages to be causally related to a complex re-orchestration of tryptophan metabolism, resulting in activation of the aryl hydrocarbon receptor. We further show that the altered metabolism of IDH-mutant gliomas maintains this axis in bystander cells and that pharmacological inhibition of tryptophan metabolism can reverse immunosuppression. In conclusion, we provide evidence of a glioma genotype-dependent intratumoral network of resident and recruited myeloid cells and identify tryptophan metabolism as a target for immunotherapy of IDH-mutant tumors.},
- author = {Friedrich, Mirco and Sankowski, Roman and Bunse, Lukas and Kilian, Michael and Green, Edward and Ramallo Guevara, Carina and Pusch, Stefan and Poschet, Gernot and Sanghvi, Khwab and Hahn, Markus and Bunse, Theresa and Münch, Philipp and Gegner, Hagen M. and Sonner, Jana K. and von Landenberg, Anna and Cichon, Frederik and Aslan, Katrin and Trobisch, Tim and Schirmer, Lucas and Abu-Sammour, Denis and Kessler, Tobias and Ratliff, Miriam and Schrimpf, Daniel and Sahm, Felix and Hopf, Carsten and Heiland, Dieter H. and Schnell, Oliver and Beck, Jürgen and Böttcher, Chotima and Fernandez-Zapata, Camila and Priller, Josef and Heiland, Sabine and Gutcher, Ilona and Quintana, Francisco J. and von Deimling, Andreas and Wick, Wolfgang and Prinz, Marco and Platten, Michael},
- copyright = {2021 The Author(s)},
- doi = {10.1038/s43018-021-00201-z},
- issn = {2662-1347},
- journal = {Nature Cancer},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Nature Publishing Group},
- pages = {1--18},
- title = {Tryptophan metabolism drives dynamic immunosuppressive myeloid states in {IDH}-mutant gliomas},
- url = {https://www.nature.com/articles/s43018-021-00201-z},
- urldate = {2021-05-30},
- year = {2021}
-}
-
-@article{gaafar_novel_2020,
- abstract = {Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.},
- author = {Gaafar, Yahya Zakaria Abdou and Ziebell, Heiko},
- doi = {10.7717/peerj.10096},
- issn = {2167-8359},
- journal = {PeerJ},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- note = {Publisher: PeerJ Inc.},
- pages = {e10096},
- shorttitle = {Novel targets for engineering {Physostegia} chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes},
- title = {Novel targets for engineering {Physostegia} chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato {microRNA} targets},
- url = {https://peerj.com/articles/10096},
- urldate = {2021-04-14},
- volume = {8},
- year = {2020}
-}
-
-@article{gao_comprehensive_2020,
- abstract = {{\textless}p{\textgreater}Mammalian DNA methylation patterns are established by two \textit{de novo} DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.{\textless}/p{\textgreater}},
- author = {Gao, Linfeng and Emperle, Max and Guo, Yiran and Grimm, Sara A. and Ren, Wendan and Adam, Sabrina and Uryu, Hidetaka and Zhang, Zhi-Min and Chen, Dongliang and Yin, Jiekai and Dukatz, Michael and Anteneh, Hiwot and Jurkowska, Renata Z. and Lu, Jiuwei and Wang, Yinsheng and Bashtrykov, Pavel and Wade, Paul A. and Wang, Gang Greg and Jeltsch, Albert and Song, Jikui},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/2020.04.27.064386},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {April},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.04.27.064386},
- title = {Comprehensive structure-function characterization of {DNMT3B} and {DNMT3A} reveals distinctive de novo {DNA} methylation mechanisms},
- url = {https://www.biorxiv.org/content/10.1101/2020.04.27.064386v1},
- urldate = {2020-05-22},
- year = {2020}
-}
-
-@article{gao_pluripotency_2020,
- abstract = {{\textless}p{\textgreater}Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyzed nucleosome positioning, H3K27 acetylation, transcription, and gastrulation rates in zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that the bulk transcriptional onset does not require Sox19b and Pou5f3, but is sensitive to their balance. Pou5f3 docks H3K27ac on the enhancers of genes involved in gastrulation and ventral fate specification. Sox19b facilitates Pou5f3 access to one-third of these enhancers. The genes regulating mesendodermal and dorsal fates are primed for activation independently on Pou5f3 and Sox19b. Strikingly, the loss of either factor results in activation of silent enhancers; simultaneous loss of both leads to premature expression of differentiation genes. Our results uncover how independent activities of maternal Pou5f3 and Sox19b add up or antagonize to determine the early gene expression repertoire.{\textless}/p{\textgreater}},
- author = {Gao, Meijiang and Veil, Marina and Rosenblatt, Marcus and Gebhard, Anna and Hass, Helge and Buryanova, Lenka and Yampolsky, Lev Y. and Grüning, Björn and Timmer, Jens and Onichtchouk, Daria},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
- doi = {10.1101/2020.02.16.949362},
- journal = {bioRxiv},
- keywords = {+Methods, +Stellar, +Tools, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.02.16.949362},
- title = {Pluripotency factors select gene expression repertoire at {Zygotic} {Genome} {Activation}},
- url = {https://www.biorxiv.org/content/10.1101/2020.02.16.949362v2},
- urldate = {2020-05-28},
- year = {2020}
-}
-
-@article{gao_pluripotency_2022,
- author = {Gao, Meijiang and Veil, Marina and Rosenblatt, Marcus and Riesle, Aileen Julia and Gebhard, Anna and Hass, Helge and Buryanova, Lenka and Yampolsky, Lev Y. and Grüning, Björn and Ulianov, Sergey V. and Timmer, Jens and Onichtchouk, Daria},
- doi = {10.1038/s41467-022-28434-1},
- journal = {Nature Communications},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation},
- url = {https://doi.org/10.1038/s41467-022-28434-1},
- volume = {13},
- year = {2022}
-}
-
-@article{garrido_identification_2020,
- abstract = {Meiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.},
- author = {Garrido, José and Aguilar, Miguel and Prieto, Pilar},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-59580-5},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {1--12},
- title = {Identification and validation of reference genes for {RT}-{qPCR} normalization in wheat meiosis},
- url = {https://www.nature.com/articles/s41598-020-59580-5},
- urldate = {2020-03-24},
- volume = {10},
- year = {2020}
-}
-
-@article{gener_full-coverage_2019,
- abstract = {Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes. Methods: Fifteen HIV-1 strains were processed with Direct RNA Sequencing (SQK-RNA002) library kits and sequenced on MinION Mk1B devices with RevD flow cells (Oxford Nanopore Technologies (ONT), Oxford, UK). Raw reads were converted to FASTQ, aligned to reference sequences, and assembled into contigs. Multi-sequence alignments of the contigs were generated and used for cladistics analysis. Results: We sequenced full-length HIV-1 from the transcriptional start site to 39 LTR (100\% virion genome) in 3 out of 15 isolates (89.6, NLAD8, AD17), achieving majority coverage (defined as \> 50\%) in another 7 out of 15 isolates. Inspection of NLAD8 sequence alignments revealed splicing or deletion signatures. Despite the strong 3′ bias, read coverage was sufficient to evaluate single-nucleotide variants (SNVs), insertions and deletions in 9 isolates, and to assemble HIV-1 genomes directly from viral RNA, achieving a maximum of 94\% assembly coverage for NLAD8. Phylogenetic relationships were maintained at the level of contigs, as well as individual reads. Conclusions: ONT native RNA sequencing performed as expected, covering full-length HIV-1 RNA without PCR or cDNA sequencing. Native single-molecule RNA sequencing supported previous models of HIV-1 replication, and samples exhibited strain-specific transcriptional signals. We propose Context Dependency Variant Classification to describe variants occurring in information-dense regions of HIV. These data provide a rich resource for emerging RNA modification detection schemes. Future work will expand HIV-1 transcript profiling to infection models and clinical samples.},
- author = {Gener, Alejandro R. and Kimata, Jason T.},
- copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/845610},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {November},
- pages = {845610},
- title = {Full-coverage native {RNA} sequencing of {HIV}-1 viruses},
- url = {https://www.biorxiv.org/content/10.1101/845610v2},
- urldate = {2019-11-26},
- year = {2019}
-}
-
-@article{genolet_identification_2020,
- abstract = {{\textless}p{\textgreater}X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Here, double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signalling pathway and delaying differentiation. To identify the genetic basis of these sex differences, we have performed a series of CRISPR knockout screens in murine embryonic stem cells to comprehensively identify X-linked genes that cause the female pluripotency phenotype. We found multiple genes that act in concert, among which Klhl13 plays a central role. We show that this E3 ubiquitin ligase substrate adaptor protein promotes pluripotency factor expression, delays differentiation and represses MAPK target genes, and we identify putative substrates. We thus elucidate the mechanisms that drive sex-induced differences in pluripotent cells with implications for gender medicine in the context of induced pluripotent stem cell based therapies.{\textless}/p{\textgreater}},
- author = {Genolet, Oriana and Monaco, Anna A. and Dunkel, Ilona and Boettcher, Michael and Schulz, Edda G.},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
- doi = {10.1101/2020.03.09.983544},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.03.09.983544},
- title = {Identification of {X}-chromosomal genes that drive global {X}-dosage effects in mammals},
- url = {https://www.biorxiv.org/content/10.1101/2020.03.09.983544v1},
- urldate = {2020-03-24},
- year = {2020}
-}
-
-@article{genolet_identification_2021,
- author = {Genolet, Oriana and Monaco, Anna A. and Dunkel, Ilona and Boettcher, Michael and Schulz, Edda G.},
- doi = {10.1186/s13059-021-02321-2},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Identification of {X}-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical {CRISPR} screening approach},
- url = {https://doi.org/10.1186/s13059-021-02321-2},
- volume = {22},
- year = {2021}
-}
-
-@article{gessara_highly_2021,
- author = {Gessara, Ivana and Dittrich, Falk and Hertel, Moritz and Hildebrand, Staffan and Pfeifer, Alexander and Frankl-Vilches, Carolina and McGrew, Mike and Gahr, Manfred},
- doi = {10.1016/j.stemcr.2021.02.015},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Elsevier BV},
- number = {4},
- pages = {784--796},
- title = {Highly {Efficient} {Genome} {Modification} of {Cultured} {Primordial} {Germ} {Cells} with {Lentiviral} {Vectors} to {Generate} {Transgenic} {Songbirds}},
- url = {https://doi.org/10.1016/j.stemcr.2021.02.015},
- volume = {16},
- year = {2021}
-}
-
-@article{gilbertson_conservation_2021,
- author = {Gilbertson, Sarah E. and Weinmann, Amy S.},
- doi = {10.1016/j.it.2021.10.007},
- journal = {Trends in Immunology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {December},
- note = {Publisher: Elsevier BV},
- number = {12},
- pages = {1077--1087},
- title = {Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis},
- url = {https://doi.org/10.1016/j.it.2021.10.007},
- volume = {42},
- year = {2021}
-}
-
-@article{gissi_13-gene_2019,
- abstract = {Background: This study aimed to evaluate the prognostic value of a non-invasive sampling procedure based on 13-gene DNA methylation analysis in the follow-up of patients previously treated for oral squamous cell carcinoma (OSCC). Methods: The study population included 49 consecutive patients treated for OSCC. Oral brushing sample collection was performed at two different times: before any cancer treatment in the tumor mass and during patient follow-up almost 6 months after OSCC treatment, within the regenerative area after OSCC resection. Each sample was considered positive or negative in relation to a predefined cut-off value. Results: Before any cancer treatment, 47/49 specimens exceeded the score and were considered as positive. Six months after OSCC resection, 16/49 specimens also had positive scores in the samples collected from the regenerative area. During the follow-up period, 7/49 patients developed locoregional relapse: 6/7 patients had a positive score in the regenerative area after OSCC resection. The presence of a positive score after oral cancer treatment was the most powerful variable related to the appearance of locoregional relapse. Conclusion: 13-gene DNA methylation analysis by oral brushing may have a clinical application as a prognostic non-invasive tool in the follow-up of patients surgically treated for OSCC.},
- author = {Gissi, Davide B. and Tarsitano, Achille and Gabusi, Andrea and Rossi, Roberto and Attardo, Giuseppe and Lenzi, Jacopo and Marchetti, Claudio and Montebugnoli, Lucio and Foschini, Maria P. and Morandi, Luca},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/jcm8122107},
- journal = {Journal of Clinical Medicine},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, bisulfite sequencing, follow-up surveillance, oral brushing, oral squamous cell carcinoma, prognosis, quantitative DNA methylation analysis},
- language = {en},
- month = {December},
- number = {12},
- pages = {2107},
- shorttitle = {13-gene {DNA} {Methylation} {Analysis} from {Oral} {Brushing}},
- title = {13-gene {DNA} {Methylation} {Analysis} from {Oral} {Brushing}: {A} {Promising} {Non} {Invasive} {Tool} in the {Follow}-up of {Oral} {Cancer} {Patients}},
- url = {https://www.mdpi.com/2077-0383/8/12/2107},
- urldate = {2019-12-21},
- volume = {8},
- year = {2019}
-}
-
-@article{gjaltema_distal_2021,
- author = {Gjaltema, Rutger A. F. and Schwämmle, Till and Kautz, Pauline and Robson, Michael and Schöpflin, Robert and Lustig, Liat Ravid and Brandenburg, Lennart and Dunkel, Ilona and Vechiatto, Carolina and Ntini, Evgenia and Mutzel, Verena and Schmiedel, Vera and Marsico, Annalisa and Mundlos, Stefan and Schulz, Edda G.},
- doi = {10.1101/2021.03.29.437476},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Distal and proximal cis-regulatory elements sense {X}-chromosomal dosage and developmental state at {theXistlocus}},
- url = {https://doi.org/10.1101/2021.03.29.437476},
- year = {2021}
-}
-
-@article{glaros_limited_2021,
- author = {Glaros, Vassilis and Rauschmeier, René and Artemov, Artem V. and Reinhardt, Annika and Ols, Sebastian and Emmanouilidi, Aikaterini and Gustafsson, Charlotte and You, Yuanyuan and Mirabello, Claudio and Björklund, Åsa K. and Perez, Laurent and King, Neil P. and Månsson, Robert and Angeletti, Davide and Loré, Karin and Adameyko, Igor and Busslinger, Meinrad and Kreslavsky, Taras},
- doi = {10.1016/j.immuni.2021.08.017},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Elsevier BV},
- number = {9},
- pages = {2005--2023.e10},
- title = {Limited access to antigen drives generation of early {B} cell memory while restraining the plasmablast response},
- url = {https://doi.org/10.1016/j.immuni.2021.08.017},
- volume = {54},
- year = {2021}
-}
-
-@article{greenfield_modification_2020,
- abstract = {Dysregulation of epigenetic processes is increasingly understood to play a role in the pathogenesis of myeloproliferative neoplasms (MPNs). Ruxolitinib, a JAK/STAT inhibitor, has proved a useful addition to the therapeutic arsenal for these disorders, but has limited disease modifying activity. We determined the effect of JAK inhibition on the histone landscape of MPN cells in cell line models of MPNs and validated using samples from the MAJIC randomised clinical trial of ruxolitinib in polycythaemia vera and essential thrombocythaemia. We demonstrated an epigenetic modifying effect of ruxolitinib using a histone modification assay. The majority of 21 histone H3 modifications were upregulated, with H3K27me3 and H3K36me2 significant in the combined cell line results. Chromatin immunoprecipitation and sequencing (CHIP-seq) for three marks of interest, H3K4me1, H3K4me3 and H3K27ac, was consistent with the histone modification assay showing a significant increase in H3K4me3 and H3K27ac peaks at promoter regions, both marks of active transcription. In contrast, RNA sequencing demonstrates a coordinated reduction in gene expression in a number of cell pathways including PI3K-AKT signalling, transcriptional misregulation in cancer and JAK-STAT signalling in spite of these histone changes. This highlights the complex mechanisms of transcriptional control within the cells which was reflected in analysis of the histone landscape in patient samples following ruxolitinib treatment.},
- author = {Greenfield, Graeme and McPherson, Suzanne and Smith, James and Mead, Adam and Harrison, Claire and Mills, Ken and McMullin, Mary Frances},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/cancers12092669},
- journal = {Cancers},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, JAK inhibition, epigenetics, histone modification, myeloproliferative neoplasms},
- language = {en},
- month = {September},
- note = {Number: 9
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {9},
- pages = {2669},
- title = {Modification of the {Histone} {Landscape} with {JAK} {Inhibition} in {Myeloproliferative} {Neoplasms}},
- url = {https://www.mdpi.com/2072-6694/12/9/2669},
- urldate = {2021-04-09},
- volume = {12},
- year = {2020}
-}
-
-@article{greve_decitabine_2021,
- abstract = {Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3–1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3–1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group.
-Significance: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813
-Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3–1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3–1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group.
-Significance: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813},
- author = {Greve, Gabriele and Schüler, Julia and Grüning, Björn A. and Berberich, Bettina and Stomper, Julia and Zimmer, Dennis and Gutenkunst, Lea and Bönisch, Ulrike and Meier, Ruth and Blagitko-Dorfs, Nadja and Grishina, Olga and Pfeifer, Dietmar and Weichenhan, Dieter and Plass, Christoph and Lübbert, Michael},
- copyright = {©2020 American Association for Cancer Research.},
- doi = {10.1158/0008-5472.CAN-20-1430},
- issn = {0008-5472, 1538-7445},
- journal = {Cancer Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- note = {Publisher: American Association for Cancer Research
-Section: Genome and Epigenome},
- number = {4},
- pages = {834--846},
- pmid = {33203699},
- shorttitle = {Decitabine {Induces} {Gene} {Derepression} on {Monosomic} {Chromosomes}},
- title = {Decitabine {Induces} {Gene} {Derepression} on {Monosomic} {Chromosomes}: {In} {Vitro} and {In} {Vivo} {Effects} in {Adverse}-{Risk} {Cytogenetics} {AML}},
- url = {https://cancerres.aacrjournals.org/content/81/4/834},
- urldate = {2021-08-19},
- volume = {81},
- year = {2021}
-}
-
-@article{gruning_rna_2017,
- author = {Grüning, Björn A. and Fallmann, Jörg and Yusuf, Dilmurat and Will, Sebastian and Erxleben, Anika and Eggenhofer, Florian and Houwaart, Torsten and Batut, Bérénice and Videm, Pavankumar and Bagnacani, Andrea and Wolfien, Markus and Lott, Steffen C. and Hoogstrate, Youri and Hess, Wolfgang R. and Wolkenhauer, Olaf and Hoffmann, Steve and Akalin, Altuna and Ohler, Uwe and Stadler, Peter F. and Backofen, Rolf},
- doi = {10.1093/nar/gkx409},
- issn = {0305-1048},
- journal = {Nucleic Acids Research},
- keywords = {+Galactic, +IsGalaxy, {\textgreater}RNA Workbench},
- month = {July},
- number = {W1},
- pages = {W560--W566},
- title = {The {RNA} workbench: best practices for {RNA} and high-throughput sequencing bioinformatics in {Galaxy}},
- url = {http://dx.doi.org/10.1093/nar/gkx409},
- volume = {45},
- year = {2017}
-}
-
-@article{gu_galaxy-ml_2021,
- abstract = {Supervised machine learning is an essential but difficult to use approach in biomedical data analysis. The Galaxy-ML toolkit (https://galaxyproject.org/community/machine-learning/) makes supervised machine learning more accessible to biomedical scientists by enabling them to perform end-to-end reproducible machine learning analyses at large scale using only a web browser. Galaxy-ML extends Galaxy (https://galaxyproject.org), a biomedical computational workbench used by tens of thousands of scientists across the world, with a suite of tools for all aspects of supervised machine learning.},
- author = {Gu, Qiang and Kumar, Anup and Bray, Simon and Creason, Allison and Khanteymoori, Alireza and Jalili, Vahid and Grüning, Björn and Goecks, Jeremy},
- doi = {10.1371/journal.pcbi.1009014},
- issn = {1553-7358},
- journal = {PLOS Computational Biology},
- keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}ML Workbench, {\textgreater}UseGalaxy.eu, Cancers and neoplasms, Decision trees, Deep learning, Galaxies, Machine learning, Medicine and health sciences, Scientists, Supervised machine learning},
- language = {en},
- month = {June},
- note = {Publisher: Public Library of Science},
- number = {6},
- pages = {e1009014},
- shorttitle = {Galaxy-{ML}},
- title = {Galaxy-{ML}: {An} accessible, reproducible, and scalable machine learning toolkit for biomedicine},
- url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009014},
- urldate = {2021-06-07},
- volume = {17},
- year = {2021}
-}
-
-@article{guendel_group_2020,
- abstract = {Solitary intestinal lymphoid tissues such as cryptopatches (CPs) and isolated lymphoid follicles (ILFs) constitute steady-state activation hubs containing group 3 innate lymphoid cells (ILC3) that continuously produce interleukin (IL)-22. The outer surface of CPs and ILFs is demarcated by a poorly characterized population of CD11c+ cells. Using genome-wide single-cell transcriptional profiling of intestinal mononuclear phagocytes and multidimensional flow cytometry, we found that CP- and ILF-associated CD11c+ cells were a transcriptionally distinct subset of intestinal cDCs, which we term CIA-DCs. CIA-DCs required programming by CP- and ILF-resident CCR6+ ILC3 via lymphotoxin-β receptor signaling in cDCs. CIA-DCs differentially expressed genes associated with immunoregulation and were the major cellular source of IL-22 binding protein (IL-22BP) at steady state. Mice lacking CIA-DC-derived IL-22BP exhibited diminished expression of epithelial lipid transporters, reduced lipid resorption, and changes in body fat homeostasis. Our findings provide insight into the design principles of an immunoregulatory checkpoint controlling nutrient absorption.},
- author = {Guendel, Fabian and Kofoed-Branzk, Michael and Gronke, Konrad and Tizian, Caroline and Witkowski, Mario and Cheng, Hung-Wei and Heinz, Gitta Anne and Heinrich, Frederik and Durek, Pawel and Norris, Paula S. and Ware, Carl F. and Ruedl, Christiane and Herold, Susanne and Pfeffer, Klaus and Hehlgans, Thomas and Waisman, Ari and Becher, Burkhard and Giannou, Anastasios D. and Brachs, Sebastian and Ebert, Karolina and Tanriver, Yakup and Ludewig, Burkhard and Mashreghi, Mir-Farzin and Kruglov, Andrey A. and Diefenbach, Andreas},
- doi = {10.1016/j.immuni.2020.10.012},
- issn = {1074-7613},
- journal = {Immunity},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, cryptopatches, dendritic cells, innate lymphoid cells, interleukin 22 binding protein, isolated lymphoid follicles, solitary intestinal lymphoid tissues},
- language = {en},
- month = {November},
- number = {5},
- pages = {1015--1032.e8},
- title = {Group 3 {Innate} {Lymphoid} {Cells} {Program} a {Distinct} {Subset} of {IL}-{22BP}-{Producing} {Dendritic} {Cells} {Demarcating} {Solitary} {Intestinal} {Lymphoid} {Tissues}},
- url = {https://www.sciencedirect.com/science/article/pii/S1074761320304532},
- urldate = {2021-02-21},
- volume = {53},
- year = {2020}
-}
-
-@article{haas_n-tp63_2019,
- abstract = {Mucociliary epithelia provide a first line of defense against pathogens. Impaired regeneration and remodeling of mucociliary epithelia are associated with dysregulated Wnt/β-catenin signaling in chronic airway diseases, but underlying mechanisms remain elusive, and studies yield seemingly contradicting results. Employing the Xenopus mucociliary epidermis, the mouse airway, and human airway Basal cells, we characterize the evolutionarily conserved roles of Wnt/β-catenin signaling in vertebrates. In multiciliated cells, Wnt is required for cilia formation during differentiation. In Basal cells, Wnt prevents specification of epithelial cell types by activating ΔN-TP63, a master transcription factor, which is necessary and sufficient to mediate the Wnt-induced inhibition of specification and is required to retain Basal cells during development. Chronic Wnt activation leads to remodeling and Basal cell hyperplasia, which are reversible in vivo and in vitro, suggesting Wnt inhibition as a treatment option in chronic lung diseases. Our work provides important insights into mucociliary signaling, development, and disease.},
- author = {Haas, Maximilian and Gómez Vázquez, José Luis and Sun, Dingyuan Iris and Tran, Hong Thi and Brislinger, Magdalena and Tasca, Alexia and Shomroni, Orr and Vleminckx, Kris and Walentek, Peter},
- doi = {10.1016/j.celrep.2019.08.063},
- issn = {2211-1247},
- journal = {Cell Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Wnt signaling, airway epithelia, basal cell, epithelia, mouse, mucociliary, multiciliated cell, β-catenin},
- language = {en},
- month = {September},
- number = {13},
- pages = {3338--3352.e6},
- title = {Δ{N}-{Tp63} {Mediates} {Wnt}/β-{Catenin}-{Induced} {Inhibition} of {Differentiation} in {Basal} {Stem} {Cells} of {Mucociliary} {Epithelia}},
- url = {http://www.sciencedirect.com/science/article/pii/S2211124719311180},
- urldate = {2019-11-06},
- volume = {28},
- year = {2019}
-}
-
-@article{hahn_dna_2020,
- abstract = {Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Dnmt1 deletion in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, DNMT1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is implicated in age- and disease- related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.},
- author = {Hahn, Anne and Pensold, Daniel and Bayer, Cathrin and Tittelmeier, Jessica and González-Bermúdez, Lourdes and Marx-Blümel, Lisa and Linde, Jenice and Groß, Jonas and Salinas-Riester, Gabriela and Lingner, Thomas and von Maltzahn, Julia and Spehr, Marc and Pieler, Tomas and Urbach, Anja and Zimmer-Bensch, Geraldine},
- doi = {10.3389/fcell.2020.00639},
- issn = {2296-634X},
- journal = {Frontiers in Cell and Developmental Biology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Aging, Cerebral Cortex, DNA Methylation, GABA, inhibitory interneurons, proteostasis, synapse, transcriptional control},
- language = {English},
- note = {Publisher: Frontiers},
- title = {{DNA} {Methyltransferase} 1 ({DNMT1}) {Function} {Is} {Implicated} in the {Age}-{Related} {Loss} of {Cortical} {Interneurons}},
- url = {https://www.frontiersin.org/articles/10.3389/fcell.2020.00639/full},
- urldate = {2021-02-08},
- volume = {8},
- year = {2020}
-}
-
-@article{hamprecht_candida_2019,
- author = {Hamprecht, Axel and Barber, Amelia E. and Mellinghoff, Sibylle C. and Thelen, Philipp and Walther, Grit and Yu, Yanying and Neurgaonkar, Priya and Dandekar, Thomas and Cornely, Oliver A. and Martin, Ronny and Kurzai, Oliver and {on behalf of the German Candida auris Study Group}},
- doi = {10.3201/eid2509.190262},
- issn = {1080-6040, 1080-6059},
- journal = {Emerging Infectious Diseases},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {September},
- number = {9},
- pages = {1763--1765},
- title = {Candida auris in {Germany} and {Previous} {Exposure} to {Foreign} {Healthcare}},
- url = {http://wwwnc.cdc.gov/eid/article/25/9/19-0262_article.htm},
- urldate = {2019-09-20},
- volume = {25},
- year = {2019}
-}
-
-@article{hering_eikenella_2021,
- author = {Hering, Silvio and Jansson, Moritz K. and Buhl, Michael E. J.},
- doi = {10.1099/ijsem.0.004977},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Microbiology Society},
- number = {9},
- title = {Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus {Eikenella} to include saccharolytic species},
- url = {https://doi.org/10.1099/ijsem.0.004977},
- volume = {71},
- year = {2021}
-}
-
-@article{hernandez_design_2020,
- abstract = {Biological control is emerging as a feasible alternative to chemical pesticides in agriculture. Measuring the microbial biocontrol agent (mBCA) populations in the environment is essential for an accurate risk assessment and to optimize the usage of an mBCA-based plant protection product. In this manuscript, a workflow to obtain a large number of qPCR markers suitable for robust strain-specific detection and quantification is presented. The workflow starts from whole genome sequencing data and consists on (i) identifying the strain-specific sequences, (ii) designing specific primer/probe sets for qPCR assays, and (iii) empirically verifying the performance of the assays. The first two stages involve exclusively computer work, but they are intended for researchers with little or no bioinformatic background: only knowledge of the BLAST suite tools and working with spreadsheets are required, and familiarity with the Galaxy environment and next-generation sequencing concepts are strongly advised. All bioinformatic work can be implemented using publically available resources and a regular desktop computer, no matter the operating system, connected to the Internet. The workflow was tested with 5 bacterial strains from different species under development as mBCAs, and yielded thousands of candidate markers and a triplex qPCR assay for each candidate mBCA. The qPCR assays were successfully tested in soils of different nature, water from different sources, and samples from different plant tissues. The mBCA detection limits and population dynamics in the different matrices are similar to those in qPCR assasys designed by other means. In summary a new accessible, amenable, cost-effective and robust, workflow to obtain a large number of strain-specific qPCR markers, is presented.},
- author = {Hernández, Iker and Sant, Clara and Martínez, Raquel and Fernández, Carolina},
- doi = {10.3389/fmicb.2020.00208},
- issn = {1664-302X},
- journal = {Frontiers in Microbiology},
- keywords = {+HowTo, +RefPublic, +Stellar, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, Bacterial strain-specific, NGS, biocontrol, marker, qPCR, risk assesment},
- language = {English},
- note = {Publisher: Frontiers},
- title = {Design of {Bacterial} {Strain}-{Specific} {qPCR} {Assays} {Using} {NGS} {Data} and {Publicly} {Available} {Resources} and {Its} {Application} to {Track} {Biocontrol} {Strains}},
- url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.00208/full},
- urldate = {2020-03-23},
- volume = {11},
- year = {2020}
-}
-
-@article{hesse_proximity_2020,
- author = {Hesse, Michael and Bednarz, Rebecca and Carls, Esther and Becker, Cora and Bondareva, Olga and Lother, Achim and Geisen, Caroline and Dreßen, Martina and Krane, Markus and Roell, Wilhelm and Hein, Lutz and Fleischmann, Bernd K. and Gilsbach, Ralf},
- doi = {10.1016/j.yjmcc.2020.11.012},
- journal = {Journal of Molecular and Cellular Cardiology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {December},
- note = {Publisher: Elsevier BV},
- title = {Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes},
- url = {https://doi.org/10.1016/j.yjmcc.2020.11.012},
- year = {2020}
-}
-
-@article{hesse_proximity_2021,
- abstract = {The adult mammalian heart consists of mononuclear and binuclear cardiomyocytes (CMs) with various ploidies. However, it remains unclear whether a variation in ploidy or number of nuclei is associated with distinct functions and injury responses in CMs, including regeneration. Therefore, we investigated transcriptomes and cellular as well as nuclear features of mononucleated and binucleated CMs in adult mouse hearts with and without injury. To be able to identify the role of ploidy we analyzed control and failing human ventricular CMs because human CMs show a larger and disease-sensitive degree of polyploidization. Using transgenic Myh6-H2BmCh to identify mononucleated and binucleated mouse CMs, we found that cellular volume and RNA content were similar in both. On average nuclei of mononuclear CMs showed a 2-fold higher ploidy, as compared to binuclear CMs indicating that most mononuclear CMs are tetraploid. After myocardial infarction mononucleated and binucleated CMs in the border zone of the lesion responded with hypertrophy and corresponding changes in gene expression, as well as a low level of induction of cell cycle gene expression. Human CMs allowed us to study a wide range of polyploidy spanning from 2n to 16n. Notably, basal as well as pathological gene expression signatures and programs in failing CMs proved to be independent of ploidy. In summary, gene expression profiles were induced in proximity to injury, but independent of number of nuclei or ploidy levels in CMs.},
- author = {Hesse, Michael and Bednarz, Rebecca and Carls, Esther and Becker, Cora and Bondareva, Olga and Lother, Achim and Geisen, Caroline and Dreßen, Martina and Krane, Markus and Roell, Wilhelm and Hein, Lutz and Fleischmann, Bernd K. and Gilsbach, Ralf},
- doi = {10.1016/j.yjmcc.2020.11.012},
- issn = {0022-2828},
- journal = {Journal of Molecular and Cellular Cardiology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Cardiac myocyte, Cell cycle, Heart disease, Number of nuclei, Ploidy},
- language = {en},
- month = {March},
- pages = {95--104},
- title = {Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes},
- url = {https://www.sciencedirect.com/science/article/pii/S0022282820303357},
- urldate = {2021-05-05},
- volume = {152},
- year = {2021}
-}
-
-@article{hetz_burkholderiaceae_2021,
- author = {Hetz, Stefanie A. and Horn, Marcus A.},
- doi = {10.3389/fmicb.2021.628269},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Frontiers Media SA},
- title = {Burkholderiaceae {Are} {Key} {Acetate} {Assimilators} {During} {Complete} {Denitrification} in {Acidic} {Cryoturbated} {Peat} {Circles} of the {Arctic} {Tundra}},
- url = {https://doi.org/10.3389/fmicb.2021.628269},
- volume = {12},
- year = {2021}
-}
-
-@article{hildebrandt_activina_2021,
- abstract = {Balanced signal transduction is crucial in tissue patterning, particularly in the vasculature. Heterotopic ossification (HO) is tightly linked to vascularization with increased vessel number in hereditary forms of HO, such as Fibrodysplasia ossificans progressiva (FOP). FOP is caused by mutations in the BMP type I receptor ACVR1 leading to aberrant SMAD1/5 signaling in response to ActivinA. Whether observed vascular phenotype in human FOP lesions is connected to aberrant ActivinA signaling is unknown. Blocking of ActivinA prevents HO in FOP mice indicating a central role of the ligand in FOP. Here, we established a new FOP endothelial cell model generated from induced pluripotent stem cells (iECs) to study ActivinA signaling. FOP iECs recapitulate pathogenic ActivinA/SMAD1/5 signaling. Whole transcriptome analysis identified ActivinA mediated activation of the BMP/NOTCH pathway exclusively in FOP iECs, which was rescued to WT transcriptional levels by the drug candidate Saracatinib. We propose that ActivinA causes transcriptional pre-patterning of the FOP endothelium, which might contribute to differential vascularity in FOP lesions compared to non-hereditary HO.},
- author = {Hildebrandt, Susanne and Kampfrath, Branka and Fischer, Kristin and Hildebrand, Laura and Haupt, Julia and Stachelscheid, Harald and Knaus, Petra},
- doi = {10.1007/s12015-020-10103-9},
- issn = {2629-3277},
- journal = {Stem Cell Reviews and Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {June},
- number = {3},
- pages = {1039--1052},
- title = {{ActivinA} {Induced} {SMAD1}/5 {Signaling} in an {iPSC} {Derived} {EC} {Model} of {Fibrodysplasia} {Ossificans} {Progressiva} ({FOP}) {Can} {Be} {Rescued} by the {Drug} {Candidate} {Saracatinib}},
- url = {https://doi.org/10.1007/s12015-020-10103-9},
- urldate = {2021-07-18},
- volume = {17},
- year = {2021}
-}
-
-@article{hille_ultrastructural_2020,
- abstract = {Background Reticulated platelets (RP) are the youngest circulating platelets in blood. An increased amount of this subpopulation is associated with higher cardiovascular risk and mortality. Objectives It is unknown to what extent intrinsic properties of RP contribute to their hyperreactive features. This study is the first providing a multifactorial approach based on ultrastructural, transcriptional, and functional analysis of RP compared to non-RP sorted by flow cytometry. Methods Reticulated platelets and non-RP were sorted after platelet staining with SYTO 13. Employing transmission electron microscopy, 1089 micrographs were analyzed for platelet size, amounts of intracellular structures, and anatomical surrogates indicating activation. Long and small RNA-sequencing (RNA-seq) were performed for analyzing differential gene expression. Functional analysis of P-selectin—an upregulated mRNA in RP—was performed in healthy subjects and patients on P2Y12-inhibitors. Results Electron micrographs uncovered distinct ultrastructural differences in RP versus non-RP. Cross sections were 1.9-fold larger in RP (P {\textless} .0001). Amounts of α-granules, dense granules, open canalicular system-openings, and mitochondria were increased in RP, which persisted after adjustment for platelet size. Long RNA-seq showed 1212 upregulated transcripts that are predominantly associated to platelet shape change, aggregation, and activation; 1264 mRNAs were downregulated in RP. Small RNA-seq did not reveal any differentially expressed transcripts. Functional analysis displayed higher P-selectin expression as compared to non-RP upon ADP- or TRAP-stimulation. Conclusions Our results demonstrate that altered intrinsic structural and molecular properties contribute to the hyperreactivity of RP. These properties and an increased amount of RP may account for the association with cardiovascular risk.},
- author = {Hille, Laura and Lenz, Maximilian and Vlachos, Andreas and Grüning, Björn and Hein, Lutz and Neumann, Franz-Josef and Nührenberg, Thomas G. and Trenk, Dietmar},
- doi = {10.1111/jth.14895},
- issn = {1538-7836},
- journal = {Journal of Thrombosis and Haemostasis},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, P-selectin, platelet activation, platelet aggregation, transcriptome analysis, transmission electron microscopy},
- language = {en},
- note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jth.14895},
- number = {8},
- pages = {2034--2046},
- title = {Ultrastructural, transcriptional, and functional differences between human reticulated and non-reticulated platelets},
- url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jth.14895},
- urldate = {2020-08-21},
- volume = {18},
- year = {2020}
-}
-
-@article{hofacker_engineering_2020,
- abstract = {Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.},
- author = {Hofacker, Daniel and Broche, Julian and Laistner, Laura and Adam, Sabrina and Bashtrykov, Pavel and Jeltsch, Albert},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/ijms21020502},
- journal = {International Journal of Molecular Sciences},
- keywords = {+Methods, +UseLocal, +UsePublic, {\textgreater}UseGalaxy.eu, DNMT3A-DNMT3L, SunTag, dCas9, epigenome editing, targeted DNA methylation},
- language = {en},
- month = {January},
- number = {2},
- pages = {502},
- title = {Engineering of {Effector} {Domains} for {Targeted} {DNA} {Methylation} with {Reduced} {Off}-{Target} {Effects}},
- url = {https://www.mdpi.com/1422-0067/21/2/502},
- urldate = {2020-01-25},
- volume = {21},
- year = {2020}
-}
-
-@article{holper_genome-wide_2021,
- author = {Hölper, Julia E. and Grey, Finn and Baillie, John Kenneth and Regan, Tim and Parkinson, Nicholas J. and Höper, Dirk and Thamamongood, Thiprampai and Schwemmle, Martin and Pannhorst, Katrin and Wendt, Lisa and Mettenleiter, Thomas C. and Klupp, Barbara G.},
- doi = {10.3390/v13081574},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: MDPI AG},
- number = {8},
- pages = {1574},
- title = {A {Genome}-{Wide} {CRISPR}/{Cas9} {Screen} {Reveals} the {Requirement} of {Host} {Sphingomyelin} {Synthase} 1 for {Infection} with {Pseudorabies} {Virus} {Mutant} {gD}–{Pass}},
- url = {https://doi.org/10.3390/v13081574},
- volume = {13},
- year = {2021}
-}
-
-@phdthesis{holthausen_bermejo_workflow-based_2019,
- abstract = {La comparación de secuencias de textos es un área de notable relevancia dentro de las Ciencias de la Computación. Existen varios problemas clásicos representativos del área, como el problema de la Subsecuencia Común de mayor Longitud, consistente en encontrar información compartida por diferentes cadenas de texto. Sus aplicaciones 
-van desde la Lingüística Computacional hasta la Bioinformática, entre otras. Al respecto de esta última, el área de la comparación de secuencias de genomas ha recibido mucha atención durante los últimos años, lo que ha llevado a un crecimiento destacado. Esto, junto a las mejoras técnicas en el rendimiento computacional, está contribuyendo a ampliar el conocimiento sobre quiénes somos. En particular, la evolución de las especies, a pesar de haber sido extensamente estudiada, sigue necesitando ser analizada, debido a su complejidad, tanto analítica como computacional. Nuevas herramientas para el estudio de Eventos Evolutivos pueden proveernos de información relevante sobre rasgos y enfermedades, además de una mayor comprensión de los mecanismos que subyacen a la evolución (que tienen un 
-impacto directo en la salud). El flujo de trabajo presentado “BlockTracer” es una herramienta que permite a los investigadores/as seleccionar una serie de cromosomas de distintas especies y buscar bloques de información directamente relacionados entre ellos. Para conseguir esto, varios programas independientes han sido creados y 
-orquestados...},
- author = {Holthausen Bermejo, Ricardo},
- copyright = {info:eu-repo/semantics/openAccess},
- keywords = {+Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, {\textgreater}BitLAB, {\textgreater}UseGalaxy.eu},
- language = {eng},
- month = {December},
- school = {Universidad de Malaga},
- title = {A workflow-based algorithm for tracing {Computational} {Synteny} {Blocks} along different species},
- url = {https://riuma.uma.es/xmlui/handle/10630/19060},
- urldate = {2020-01-23},
- year = {2019}
-}
-
-@article{jalili_galaxy_2020,
- abstract = {Abstract.  Galaxy (https://galaxyproject.org) is a web-based computational workbench used by tens of thousands of scientists across the world to analyze large b},
- author = {Jalili, Vahid and Afgan, Enis and Gu, Qiang and Clements, Dave and Blankenberg, Daniel and Goecks, Jeremy and Taylor, James and Nekrutenko, Anton},
- doi = {10.1093/nar/gkaa434},
- issn = {0305-1048},
- journal = {Nucleic Acids Research},
- keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Live EU, {\textgreater}Metabolomics EU, {\textgreater}Metagenomics EU, {\textgreater}Proteomics EU, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {July},
- note = {Publisher: Oxford Academic},
- number = {W1},
- pages = {W395--W402},
- shorttitle = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses},
- title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2020 update},
- url = {https://academic.oup.com/nar/article/48/W1/W395/5849904},
- urldate = {2020-08-20},
- volume = {48},
- year = {2020}
-}
-
-@article{jude_draft_2019,
- abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.},
- author = {Jude, Brooke A.},
- doi = {10.1128/MRA.00683-19},
- editor = {Dunning Hotopp, Julie C.},
- issn = {2576-098X},
- journal = {Microbiology Resource Announcements},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- number = {35},
- pages = {e00683--19, /mra/8/35/MRA.00683--19.atom},
- title = {Draft {Genome} {Sequence} of a {Chitinimonas} {Species} from {Hudson} {Valley} {Waterways} {That} {Expresses} {Violacein} {Pigment}},
- url = {http://genomea.asm.org/lookup/doi/10.1128/MRA.00683-19},
- urldate = {2019-09-20},
- volume = {8},
- year = {2019}
-}
-
-@article{kaiser_mutational_2021,
- author = {Kaiser, Vera B. and Talmane, Lana and Kumar, Yatendra and Semple, Fiona and MacLennan, Marie and FitzPatrick, David R. and Taylor, Martin S. and and, Colin A. Semple},
- doi = {10.1101/2021.06.10.447556},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome},
- url = {https://doi.org/10.1101/2021.06.10.447556},
- year = {2021}
-}
-
-@article{kalmbach_genome-wide_2019,
- abstract = {The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in \textit{ARID1B}. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14$^{\textrm{+}}$ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous \textit{ARID1B} mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14$^{\textrm{+}}$ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14$^{\textrm{+}}$ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.},
- author = {Kalmbach, Alexander and Schröder, Christopher and Klein-Hitpass, Ludger and Nordström, Karl and Ulz, Peter and Heitzer, Ellen and Speicher, Michael R. and Rahmann, Sven and Wieczorek, Dagmar and Horsthemke, Bernhard and Bramswig, Nuria C.},
- doi = {10.1159/000503266},
- issn = {1424-8581, 1424-859X},
- journal = {Cytogenetic and Genome Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {english},
- number = {1},
- pages = {1--11},
- pmid = {31658463},
- title = {Genome-{Wide} {Analysis} of the {Nucleosome} {Landscape} in {Individuals} with {Coffin}-{Siris} {Syndrome}},
- url = {https://www.karger.com/Article/FullText/503266},
- urldate = {2019-11-26},
- volume = {159},
- year = {2019}
-}
-
-@article{katsanos_gene_2021,
- author = {Katsanos, Dimitris and Ferrando-Marco, Mar and Razzaq, Iqrah and Aughey, Gabriel and Southall, Tony D. and Barkoulas, Michalis},
- doi = {10.1242/dev.199452},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: The Company of Biologists},
- number = {17},
- title = {Gene expression profiling of epidermal cell types in {C}. elegans using {Targeted} {DamID}},
- url = {https://doi.org/10.1242/dev.199452},
- volume = {148},
- year = {2021}
-}
-
-@article{katsanos_targeted_2022,
- author = {Katsanos, Dimitris and Barkoulas, Michalis},
- doi = {10.1126/sciadv.abk3141},
- journal = {Science Advances},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: American Association for the Advancement of Science (AAAS)},
- number = {5},
- title = {Targeted {DamID} in {C}. elegans reveals a direct role for {LIN}-22 and {NHR}-25 in antagonizing the epidermal stem cell fate},
- url = {https://doi.org/10.1126/sciadv.abk3141},
- volume = {8},
- year = {2022}
-}
-
-@article{kavas_genome-wide_2021,
- author = {Kavas, Musa and Yıldırım, Kubilay and Seçgin, Zafer and Abdulla, Mohamed Farah and Gökdemir, Gökhan},
- doi = {10.1007/s12298-021-01052-9},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {9},
- pages = {1885--1902},
- title = {Genome-wide identification of the {BURP} domain-containing genes in {Phaseolus} vulgaris},
- url = {https://doi.org/10.1007/s12298-021-01052-9},
- volume = {27},
- year = {2021}
-}
-
-@article{king_resistome_2021,
- author = {King, T. L. and Schmidt, S. and Thakur, S. and Fedorka-Cray, P. and Keelara, S. and Harden, L. and Essack, S. Y.},
- doi = {10.1016/j.jgar.2021.01.004},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Elsevier BV},
- pages = {321--324},
- title = {Resistome of a carbapenemase-producing novel {ST232} {Klebsiella} michiganensis isolate from urban hospital effluent in {South} {Africa}},
- url = {https://doi.org/10.1016/j.jgar.2021.01.004},
- volume = {24},
- year = {2021}
-}
-
-@article{klein_pruriception_2021,
- author = {Klein, Amanda and Solinski, Hans Jürgen and Malewicz, Nathalie M. and Ieong, Hada Fong-ha and Sypek, Elizabeth I. and Shimada, Steven G. and Hartke, Timothy V. and Wooten, Matthew and Wu, Gang and Dong, Xinzhong and Hoon, Mark A. and LaMotte, Robert H. and Ringkamp, Matthias},
- doi = {10.7554/elife.64506},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: eLife Sciences Publications, Ltd},
- title = {Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates},
- url = {https://doi.org/10.7554/elife.64506},
- volume = {10},
- year = {2021}
-}
-
-@article{koeppel_sars-cov-2_2022,
- author = {Koeppel, Katja Natalie and Mendes, Adriano and Strydom, Amy and Rotherham, Lia and Mulumba, Misheck and Venter, Marietjie},
- doi = {10.3390/v14010120},
- journal = {Viruses},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: MDPI AG},
- number = {1},
- pages = {120},
- title = {{SARS}-{CoV}-2 {Reverse} {Zoonoses} to {Pumas} and {Lions}, {South} {Africa}},
- url = {https://doi.org/10.3390/v14010120},
- volume = {14},
- year = {2022}
-}
-
-@article{kolosov_malpighian_2019,
- abstract = {Skip to Next Section
-The Malpighian tubules (MTs) and hindgut constitute the functional kidney of insects. MTs are outpouchings of the gut and in most insects demonstrate proximodistal heterogeneity in function. In most insects, such heterogeneity is confined to ion/fluid secretion in the distal portion and ion/fluid reabsorption in the proximal portion. In contrast, MTs of larval Lepidoptera (caterpillars of butterflies and moths) are composed of five regions that differ in their association with the gut, their structure and ion/fluid transport function. Recent studies have shown that several regions can rapidly and reversibly switch between ion secretion and reabsorption. The present study employed RNAseq, pharmacology and electrophysiology to characterize four distinct regions of the MT in larval Trichoplusia ni. Luminal microelectrode measurements indicate changes in [K+], [Na+] and pH as fluid passes through different regions of the tubule. In addition, the regions examined differ in gene ontology enrichment, and demonstrate robust gradients in expression of ion transporters and endocrine ligand receptors. Lastly, the study provides evidence for direct involvement of voltage- and ligand-gated ion channels in epithelial ion transport of insect MTs.},
- author = {Kolosov, Dennis and O'Donnell, Michael J.},
- copyright = {© 2019. Published by The Company of Biologists Ltd. http://www.biologists.com/user-licence-1-1/},
- doi = {10.1242/jeb.211623},
- issn = {0022-0949, 1477-9145},
- journal = {Journal of Experimental Biology},
- keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {November},
- number = {22},
- pmid = {31636157},
- shorttitle = {Malpighian tubules of caterpillars},
- title = {Malpighian tubules of caterpillars: blending {RNAseq} and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms},
- url = {https://jeb.biologists.org/content/222/22/jeb211623},
- urldate = {2020-01-04},
- volume = {222},
- year = {2019}
-}
-
-@phdthesis{konovalovas_molecular_2018,
- author = {Konovalovas, Aleksandras},
- keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu},
- school = {Vilnius University},
- title = {Molecular determinants of {Totiviridae} family viruses of {Saccharomyces} sensu stricto clade},
- url = {https://epublications.vu.lt/object/elaba:31252887/index.html},
- urldate = {2019-03-23},
- year = {2018}
-}
-
-@article{kumar_community_2020,
- abstract = {Citizen Science has come up to perform analytics over the SARS-CoV-2 genome. Public GALAXY servers provide an automated platform for genomics analysis. Study includes design of GALAXY workflows for RNASEQ assembly and annotation as well as genomic variant discovery and perform analysis across four samples of SARS-CoV-2 infected humans obtained from the local population of Wuhan, China. It provides information about transcriptomics and genomic variants across the SARS-CoV-2 genome. Study can be extended to perform evolutionary and comparative study across each species of coronaviruses. Augmented and integrated study with cheminformatics and immunoinformatics will be a way forward for drug discovery and vaccine development.},
- author = {Kumar, Ambarish and Bangash, Ali Haider and Gruening, Bjoern},
- doi = {10.20944/preprints202005.0343.v1},
- journal = {Preprints},
- keywords = {+IsGalaxy, +Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Preprints},
- shorttitle = {Community {Research} {Amid} {COVID}-19 {Pandemic}},
- title = {Community {Research} {Amid} {COVID}-19 {Pandemic}: {Genomics} {Analysis} of {SARS}-{CoV}-2 over {Public} {GALAXY} server},
- url = {https://www.preprints.org/manuscript/202005.0343/v1},
- urldate = {2020-05-24},
- year = {2020}
-}
-
-@article{kumar_polycomb_2020,
- author = {Kumar, Amit and Kondhare, Kirtikumar R. and Malankar, Nilam N. and Banerjee, Anjan K.},
- doi = {10.1093/jxb/eraa468},
- editor = {Wellmer, Frank},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {October},
- note = {Publisher: Oxford University Press (OUP)},
- number = {2},
- pages = {426--444},
- title = {The {Polycomb} group methyltransferase {StE}(z)2 and deposition of {H3K27me3} and {H3K4me3} regulate the expression of tuberization genes in potato},
- url = {https://doi.org/10.1093/jxb/eraa468},
- volume = {72},
- year = {2020}
-}
-
-@article{kumar_polycomb_2021,
- abstract = {Polycomb repressive complex (PRC) group proteins regulate various developmental processes in plants by repressing target genes via H3K27 trimethylation, and they function antagonistically with H3K4 trimethylation mediated by Trithorax group proteins. Tuberization in potato has been widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1, a PRC2 member, alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2, a potential H3K27 methyltransferase in potato. Here, we demonstrate that a short-day photoperiod influences StE(z)2 expression in the leaves and stolons. StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhances yield. ChIP-sequencing using stolons induced by short-days indicated that several genes related to tuberization and phytohormones, such as StBEL5/11/29, StSWEET11B, StGA2OX1, and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we observed that another important tuberization gene, StSP6A, is targeted by StE(z)2 in leaves and that it has increased deposition of H3K27me3 under long-day (non-induced) conditions compared to short days. Overall, our results show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks might regulate the expression of key tuberization genes in potato.},
- author = {Kumar, Amit and Kondhare, Kirtikumar R and Malankar, Nilam N and Banerjee, Anjan K},
- doi = {10.1093/jxb/eraa468},
- issn = {0022-0957},
- journal = {Journal of Experimental Botany},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- number = {2},
- pages = {426--444},
- title = {The {Polycomb} group methyltransferase {StE}(z)2 and deposition of {H3K27me3} and {H3K4me3} regulate the expression of tuberization genes in potato},
- url = {https://doi.org/10.1093/jxb/eraa468},
- urldate = {2021-05-12},
- volume = {72},
- year = {2021}
-}
-
-@article{kumar_quantp:_2018,
- abstract = {Next-generation sequencing technologies, coupled to advances in mass-spectrometry-based proteomics, have facilitated system-wide quantitative profiling of expressed mRNA transcripts and proteins. Proteo-transcriptomic analysis compares the relative abundance levels of transcripts and their corresponding proteins, illuminating discordant gene product responses to perturbations. These results reveal potential post-transcriptional regulation, providing researchers with important new insights into underlying biological and pathological disease mechanisms. To carry out proteo-transcriptomic analysis, researchers require software that statistically determines transcript–protein abundance correlation levels and provides results visualization and interpretation functionality, ideally within a flexible, user-friendly platform. As a solution, we have developed the QuanTP software within the Galaxy platform. The software offers a suite of tools and functionalities critical for proteo-transcriptomics, including statistical algorithms for assessing the correlation between single transcript–protein pairs as well as across two cohorts, outlier identification and clustering, along with a diverse set of results visualizations. It is compatible with analyses of results from single experiment data or from a two-cohort comparison of aggregated replicate experiments. The tool is available in the Galaxy Tool Shed through a cloud-based instance and a Docker container. In all, QuanTP provides an accessible and effective software resource, which should enable new multiomic discoveries from quantitative proteo-transcriptomic data sets.},
- author = {Kumar, Praveen and Panigrahi, Priyabrata and Johnson, James and Weber, Wanda J. and Mehta, Subina and Sajulga, Ray and Easterly, Caleb and Crooker, Brian A. and Heydarian, Mohammad and Anamika, Krishanpal and Griffin, Timothy J. and Jagtap, Pratik D.},
- doi = {10.1021/acs.jproteome.8b00727},
- issn = {1535-3893},
- journal = {Journal of Proteome Research},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}Galaxy-P, {\textgreater}QuanTP, {\textgreater}UseGalaxy.eu},
- month = {December},
- shorttitle = {{QuanTP}},
- title = {{QuanTP}: {A} {Software} {Resource} for {Quantitative} {Proteo}-{Transcriptomic} {Comparative} {Data} {Analysis} and {Informatics}},
- url = {https://doi.org/10.1021/acs.jproteome.8b00727},
- urldate = {2019-01-24},
- year = {2018}
-}
-
-@article{kumar_tool_2021,
- abstract = {Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.A model is developed to recommend tools using a deep learning approach by analysing workflows composed by researchers on the European Galaxy server. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units neural network, a variant of a recurrent neural network. In the neural network training, the weights of tools used are derived from their usage frequencies over time and the sequences of tools are uniformly sampled from training data. Hyperparameters of the neural network are optimized using Bayesian optimization. Mean accuracy of 98\% in recommending tools is achieved for the top-1 metric.The model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface integrations on the European Galaxy server. High-quality and highly used tools are shown at the top of the recommendations. The scripts and data to create the recommendation system are available under MIT license at https://github.com/anuprulez/galaxy\_tool\_recommendation.},
- author = {Kumar, Anup and Rasche, Helena and Grüning, Björn and Backofen, Rolf},
- doi = {10.1093/gigascience/giaa152},
- issn = {2047-217X},
- journal = {GigaScience},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}UseGalaxy.eu},
- month = {January},
- number = {giaa152},
- title = {Tool recommender system in {Galaxy} using deep learning},
- url = {https://doi.org/10.1093/gigascience/giaa152},
- urldate = {2021-02-06},
- volume = {10},
- year = {2021}
-}
-
-@article{kumaran_draft_2020,
- abstract = {In the present study, we report the draft genome of soil isolate DP-K7 that has the potential to degrade methyl red. The 16S rRNA gene sequencing and whole-genome analysis exposed that the bacterial strain DP-K7 belongs to the species Kocuria indica. The genome annotation of the strain DP-K7 through the bioinformatics tool “Prokka” showed that the genome contains 3,010,594 bp with 69.01\% GC content. The genome comprises 57 contigs including 2 rRNA genes, 47 tRNA genes, and 2754 CDS. The plate and broth assay showed that the strain DP-K7 has the potential to utilize methyl red as the sole carbon source for growth. Indeed, the RP-HPLC analysis proved that the strain DP-K7 is capable of degrading methyl red. The genome BLAST against a characterized azoreductase (AzoB—Xenophilus azovorans KF46F) revealed the presence of two azoreductase-like genes (azoKi-1 and azoKi-2). The phylogenetic analysis of the primary amino acid sequence of characterized azoreductases suggested that AzoKi-1 and AzoKi-2 belong to members of the clade IV azoreductase, which are flavin-independent. The multiple sequence alignment of AzoKi-1 and AzoKi-2 with flavin-independent azoreductases showed the presence of NAD(P)H binding like motif (GxxGxxG). In addition, other genes coding for dye degrading enzymes (SodC, SodA, KatA, KatE, and DyP2) were also found in the genome supporting that the strain K. indica DP-K7 is a potential azo dye degrader.},
- author = {Kumaran, Selvapravin and Ngo, Anna Christina R. and Schultes, Fabian Peter Josef and Tischler, Dirk},
- doi = {10.1007/s13205-020-2136-3},
- issn = {2190-5738},
- journal = {3 Biotech},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- number = {4},
- pages = {175},
- title = {Draft genome sequence of {Kocuria} indica {DP}-{K7}, a methyl red degrading actinobacterium},
- url = {https://doi.org/10.1007/s13205-020-2136-3},
- urldate = {2020-04-10},
- volume = {10},
- year = {2020}
-}
-
-@article{kumaran_vitro_2022,
- author = {Kumaran, Selvapravin and Ngo, Anna Christina R. and Schultes, Fabian P. J. and Saravanan, Venkatakrishnan Sivaraj and Tischler, Dirk},
- doi = {10.1016/j.ygeno.2022.01.003},
- journal = {Genomics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Elsevier BV},
- number = {2},
- pages = {110266},
- title = {In vitro and in silico analysis of {Brilliant} {Black} degradation by {Actinobacteria} and a {Paraburkholderia} sp.},
- url = {https://doi.org/10.1016/j.ygeno.2022.01.003},
- volume = {114},
- year = {2022}
-}
-
-@article{lahm_congenital_2020,
- author = {Lahm, Harald and Jia, Meiwen and Dreßen, Martina and Wirth, Felix F. M. and Puluca, Nazan and Gilsbach, Ralf and Keavney, Bernard and Cleuziou, Julie and Beck, Nicole and Bondareva, Olga and Dzilic, Elda and Burri, Melchior and König, Karl C. and Ziegelmüller, Johannes A. and Abou-Ajram, Claudia and Neb, Irina and Zhang, Zhong and Doppler, Stefanie A. and Mastantuono, Elisa and Lichtner, Peter and Eckstein, Gertrud and Hörer, Jürgen and Ewert, Peter and Priest, James R. and Hein, Lutz and Lange, Rüdiger and Meitinger, Thomas and Cordell, Heather J. and Müller-Myhsok, Bertram and Krane, Markus},
- doi = {10.1172/JCI141837},
- issn = {0021-9738},
- journal = {The Journal of Clinical Investigation},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {November},
- note = {Publisher: American Society for Clinical Investigation},
- pmid = {0},
- title = {Congenital heart disease risk loci identified by genome-wide association study in {European} patients},
- url = {https://www.jci.org/articles/view/141837},
- urldate = {2021-01-12},
- year = {2020}
-}
-
-@article{lahm_genome-wide_2020,
- abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Rationale{\textless}/h3{\textgreater} {\textless}p{\textgreater}Genetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Objective{\textless}/h3{\textgreater} {\textless}p{\textgreater}Identification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Genetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, \textit{p}=5.28×10$^{\textrm{−9}}$) and was also indicative for septal defects (OR:2.16, \textit{p}=6.15×10$^{\textrm{−8}}$). One region on chromosome 20 pointing to the \textit{MACROD2} locus, identified four SNPs (rs150246290,OR:3.78, \textit{p}=1.27×10$^{\textrm{−10}}$; rs149890280,OR:3.74, \textit{p}=1.8×10$^{\textrm{−10}}$; rs149467721,OR:3.53; \textit{p}=1.39×10$^{\textrm{−9}}$, rs77094733,OR:3.53, \textit{p}=1.73×10$^{\textrm{−9}}$) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at \textit{ZBTB10} (rs148563140,OR:3.42, \textit{p}=3.28×10$^{\textrm{−8}}$; rs143638934,OR:3.42, \textit{p}=3.51×10$^{\textrm{−8}}$) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, \textit{p}=9.95×10$^{\textrm{−8}}$; rs11874,OR:1.60, \textit{p}=6.64×10$^{\textrm{−8}}$; rs17677363,OR:1.60, \textit{p}=9.81×10$^{\textrm{−8}}$) within the \textit{GOSR2} locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of \textit{WNT3}, and variant rs870142 related to septal defects is proposed to influence expression of \textit{MSX1}. Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for \textit{MACROD2, GOSR2, WNT3} and \textit{MSX1} at all developmental stages.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}For the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage.{\textless}/p{\textgreater}},
- author = {Lahm, Harald and Jia, Meiwen and Dreßen, Martina and Wirth, Felix and Puluca, Nazan and Gilsbach, Ralf and Keavney, Bernard D. and Cleuziou, Julie and Beck, Nicole and Bondareva, Olga and Dzilic, Elda and Burri, Melchior and König, Karl C. and Ziegelmüller, Johannes A. and Abou-Ajram, Claudia and Neb, Irina and Zhang, Zhong and Doppler, Stefanie A. and Mastantuono, Elisa and Lichtner, Peter and Eckstein, Gertrud and Hörer, Jürgen and Ewert, Peter and Priest, James R. and Hein, Lutz and Lange, Rüdiger and Meitinger, Thomas and Cordell, Heather J. and Müller-Myhsok, Bertram and Krane, Markus},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/2020.06.19.161067},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {June},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.06.19.161067},
- title = {Genome-wide association study in {European} patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart},
- url = {https://www.biorxiv.org/content/10.1101/2020.06.19.161067v1},
- urldate = {2020-08-18},
- year = {2020}
-}
-
-@article{lambrecht_interplay_2019,
- abstract = {The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.},
- author = {Lambrecht, S. Joke and Kanesaki, Yu and Fuss, Janina and Huettel, Bruno and Reinhardt, Richard and Steglich, Claudia},
- copyright = {2019 The Author(s)},
- doi = {10.1038/s41598-019-49881-9},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- number = {1},
- pages = {1--15},
- title = {Interplay and {Targetome} of the {Two} {Conserved} {Cyanobacterial} {sRNAs} {Yfr1} and {Yfr2} in {Prochlorococcus} {MED4}},
- url = {https://www.nature.com/articles/s41598-019-49881-9},
- urldate = {2019-11-06},
- volume = {9},
- year = {2019}
-}
-
-@article{lange_expression_2020,
- abstract = {SARS-CoV-2 is assumed to use angiotensin-converting enzyme 2 (ACE2) and other auxiliary proteins for cell entry. Recent studies have described conjunctival congestion in 0.8\% of patients with laboratory-confirmed SARS-CoV-2, and there has been speculation that SARS-CoV-2 can be transmitted through the conjunctiva. However, it is currently unclear whether conjunctival epithelial cells express ACE2 and its cofactors. In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high-throughput RNA sequencing to assess mRNA expression of the SARS-CoV-2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. ACE2 protein expression was assessed in eight healthy conjunctival samples using immunohistochemistry. Our results show that the SARS-CoV-2 receptor ACE2 is not substantially expressed in conjunctival samples on the mRNA (median 0.0 transcripts per million (TPM), min 0.0 TPM, max 1.7 TPM) and protein levels. Similar results were obtained for the transcription of other auxiliary molecules. In conclusion, this study finds no evidence for a significant expression of ACE2 and its auxiliary mediators for cell entry in conjunctival samples, making conjunctival infection with SARS-CoV-2 via these mediators unlikely. This article is protected by copyright. All rights reserved.},
- author = {Lange, Clemens and Wolf, Julian and Auw‐Haedrich, Claudia and Schlecht, Anja and Boneva, Stefaniya and Lapp, Thabo and Horres, Ralf and Agostini, Hansjürgen and Martin, Gottfried and Reinhard, Thomas and Schlunck, Günther},
- copyright = {This article is protected by copyright. All rights reserved.},
- doi = {10.1002/jmv.25981},
- issn = {1096-9071},
- journal = {Journal of Medical Virology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, ACE2, COVID-19, SARS-CoV-2, TMPRSS2, human conjunctiva},
- language = {en},
- month = {May},
- note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.25981},
- number = {n/a},
- title = {Expression of the {COVID}-19 receptor {ACE2} in the human conjunctiva},
- url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25981},
- urldate = {2020-05-22},
- volume = {n/a},
- year = {2020}
-}
-
-@article{larsen_identification_2019,
- abstract = {C-type lectin-like domain containing proteins (CTLDcps) mainly bind carbohydrate-based ligands, but also other ligands. CTLDcps are involved in several biological processes including cell adhesion, cell-cell interactions, and pathogen recognition. Pathogen recognition by myeloid cells, e.g. dendritic cells (DCs), can be facilitated through cell surface expressed CTLDcps. Cell surface expressed CTLDcps have been exploited in vaccine designs for specific targeting of human and mouse DCs using antibodies. In recent years, however, DC targeting using carbohydrate-based vaccines has gained interest due to low production cost, limited immunogenicity, and possibility of multivalent adjustment. In chicken, however, only a few CTLDcps have been identified. Identifying and annotating additional chicken CTLDcps (chCTLDcps) is needed to exploit carbohydrate-mediated DC targeting in chicken. Therefore, we searched the chicken GRCg6a assembly for novel chCTLDcps. We identified 28 chCTLDcps of which 10 had previously been described and also experimentally validated. RNA-seq and RT-qPCR confirmed mRNA expression of the remaining 18 identified chCTLDcps. A group of highly related chCTLDcps, moreover, was shown to be avian-specific and comprise novel members mapped to the proposed chicken natural killer gene complex. Two chCTLDcps, chCLEC17AL-A and chCLEC17AL-B, were found to share a recent common ancestor with CLEC17A. Putative mannose or fucose-binding sequence motifs, EPN and WND, were found in the CTLD of chCLEC17AL-A. Both contained intracellular internalisation and signalling sequence motifs. In conclusion, several chCTLDcps were identified and their expression confirmed. Both chCLEC17AL-A and -B showed promise as potential targets in carbohydrate-based chicken vaccine strategies. Determination of DC-specific expression of chCLEC17AL-A and -B, thus, might prove useful in chicken vaccinology.},
- author = {Larsen, Frederik T. and Bed’Hom, Bertrand and Guldbrandtsen, Bernt and Dalgaard, Tina S.},
- doi = {10.1016/j.molimm.2019.07.022},
- issn = {0161-5890},
- journal = {Molecular Immunology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, C-type lectin-like domain, Chicken, Chicken NKC, Containing proteins, Pattern-Recognition receptors, Vaccine design},
- month = {October},
- pages = {216--225},
- title = {Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies},
- url = {http://www.sciencedirect.com/science/article/pii/S0161589019304407},
- urldate = {2019-08-24},
- volume = {114},
- year = {2019}
-}
-
-@article{lastic_entropic_2020,
- abstract = {Background: Traditional omic analysis relies on p-value and fold change as selection criteria. There is an ongoing debate on their effectiveness in delivering systemic and robust interpretation, due to their dependence on assumptions of conformity with various parametric distributions.Here, we propose a threshold-free selection method based on robust, non-parametric statistics, ensuring independence from the statistical distribution properties and broad applicability. Such methods could adapt to different initial data distributions, contrary to statistical techniques based on fixed thresholds. Methods: Our work extends the Rank Products methodology with a neutral selection method of high information-extraction capacity. We introduce the calculation of the RP distribution\’s entropy to isolate the features of interest by their contribution to the distribution\’s information content. The aim is a methodology performing threshold-free identification of the differentially expressed features, which are highly informative about the phenomenon under scrutiny. Conclusions: Applying the proposed method on microarray (transcriptomic and DNA methylation) and RNAseq count data of varying sizes and noise presence, we observe robust convergence for the different parameterisations to stable cutoff points. Functional analysis through BioInfoMiner and EnrichR was used to evaluate the information potency of the resulting feature lists. Overall, the derived functional terms provide a systemic description highly compatible with the results of traditional statistical hypothesis testing techniques. The methodology behaves consistently across different data types. The feature lists are compact and information-rich, indicating phenotypic aspects specific to the tissue and biological phenomenon i nvestigated. Selection by information content measures efficiently addresses problems, emerging from arbitrary thresholding, thus facilitating the full automation of the analysis.},
- author = {Lastic, Hector-Xavier de and Liampa, Irene and Georgakilas, Alexandros G. and Zervakis, Michalis and Chatziioannou, Aristotelis},
- doi = {10.20944/preprints202009.0424.v1},
- journal = {Preprints},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {September},
- note = {Publisher: Preprints},
- shorttitle = {Entropic {Ranks}},
- title = {Entropic {Ranks}: {A} {Methodology} for {Enhanced}, {Threshold}-{Free}, {Information}-{Rich} {Data} {Partition} and {Interpretation}},
- url = {https://www.preprints.org/manuscript/202009.0424/v1},
- urldate = {2021-02-11},
- year = {2020}
-}
-
-@article{lengfelder_complex_2019,
- abstract = {Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10-/-) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10-/- mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (∆eutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10-/- mice. However, replacement of the E. faecalis wild type bacteria by a ∆eutVW mutant in SIHUMI-colonized IL-10-/- mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10-/- mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis towards a protective function.},
- author = {Lengfelder, Isabella and Sava, Irina G. and Hansen, Jonathan J. and Kleigrewe, Karin and Herzog, Jeremy and Neuhaus, Klaus and Hofmann, Thomas and Sartor, R. Balfour and Haller, Dirk},
- doi = {10.3389/fimmu.2019.01420},
- issn = {1664-3224},
- journal = {Frontiers in Immunology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Enterococcus faecalis, Ethanolamine utilization, IBD – Inflammatory bowel diseases, IL-10 deficient mice, Microbial consortium, RNA sequencing (RNAseq), SIHUMI, gnotobiotic mouse model},
- language = {English},
- title = {Complex {Bacterial} {Consortia} {Reprogram} the {Colitogenic} {Activity} of {Enterococcus} faecalis in a {Gnotobiotic} {Mouse} {Model} of {Chronic}, {Immune}-{Mediated} {Colitis}},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2019.01420/full},
- urldate = {2019-07-25},
- volume = {10},
- year = {2019}
-}
-
-@article{lezameta_draft_2020,
- abstract = {Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.},
- author = {Lezameta, Lizet and Cuicapuza, Diego and Dávila-Barclay, Alejandra and Torres, Susan and Salvatierra, Guillermo and Tsukayama, Pablo and Tamariz, Jesús},
- copyright = {Copyright © 2020 Lezameta et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.},
- doi = {10.1128/MRA.00788-20},
- issn = {2576-098X},
- journal = {Microbiology Resource Announcements},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {September},
- note = {Publisher: American Society for Microbiology
-Section: Genome Sequences},
- number = {39},
- pmid = {32972938},
- title = {Draft {Genome} {Sequence} of a {New} {Delhi} {Metallo}-β-{Lactamase} ({NDM}-1)-{Producing} {Providencia} stuartii {Strain} {Isolated} in {Lima}, {Peru}},
- url = {https://mra.asm.org/content/9/39/e00788-20},
- urldate = {2021-02-08},
- volume = {9},
- year = {2020}
-}
-
-@article{li_mitochondrial_2021,
- author = {Li, X.-Y. and Liu, Y.-C. and Zhang, R.-S. and Chen, D.-B. and Chen, M.-M. and Li, Y.-P. and Liu, Y.-Q. and Qin, L.},
- doi = {10.3920/jiff2020.0054},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Wageningen Academic Publishers},
- number = {2},
- pages = {233--243},
- title = {The mitochondrial genome of {Qinghuang}\_1, the first modern improved strain of {Chinese} oak silkworm, {Antheraea} pernyi ({Lepidoptera}: {Saturniidae})},
- url = {https://doi.org/10.3920/jiff2020.0054},
- volume = {7},
- year = {2021}
-}
-
-@article{liang_reciprocal_2020,
- abstract = {Podocyte maintenance and stress resistance are exquisitely based on high basal rates of autophagy making these cells a unique model to unravel mechanisms of autophagy regulation. Polyamines have key cellular functions such as proliferation, nucleic acid biosynthesis and autophagy. Here we test whether endogenous spermidine signaling is a driver of basal and dynamic autophagy in podocytes by using genetic and pharmacologic approaches to interfere with different steps of polyamine metabolism. Translational studies revealed altered spermidine signaling in focal segmental glomerulosclerosis in vivo and in vitro. Exogenous spermidine supplementation emerged as new treatment strategy by successfully activating autophagy in vivo via inhibition of EP300, a protein with an essential role in controlling cell growth, cell division and prompting cells to differentiate to take on specialized functions. Surprisingly, gas chromatography-mass spectroscopy based untargeted metabolomics of wild type and autophagy deficient primary podocytes revealed a positive feed-back mechanism whereby autophagy itself maintains polyamine metabolism and spermidine synthesis. The transcription factor MAFB acted as an upstream regulator of polyamine metabolism. Thus, our data highlight a novel positive feedback loop of autophagy and spermidine signaling allowing maintenance of high basal levels of autophagy as a key mechanism to sustain the filtration barrier. Hence, spermidine supplementation may emerge as a new therapeutic to restore autophagy in glomerular disease.},
- author = {Liang, Wei and Yamahara, Kosuke and Hernando-Erhard, Camila and Lagies, Simon and Wanner, Nicola and Liang, Huan and Schell, Christoph and Kammerer, Bernd and Huber, Tobias B. and Bork, Tillmann},
- doi = {10.1016/j.kint.2020.06.016},
- issn = {0085-2538},
- journal = {Kidney International},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, LC3, MAFB, autophagy, podocyte, polyamine, spermidine},
- language = {en},
- month = {June},
- title = {A {RECIPROCAL} {REGULATION} {OF} {SPERMIDINE} {AND} {AUTOPHAGY} {IN} {PODOCYTES} {MAINTAINS} {THE} {FILTRATION} {BARRIER}},
- url = {http://www.sciencedirect.com/science/article/pii/S0085253820307158},
- urldate = {2020-08-12},
- year = {2020}
-}
-
-@article{liu_denovoprofiling_2021,
- abstract = {With the advances of deep learning techniques, various architectures for molecular generation have been proposed for de novo drug design. Successful cases from academia and industrial demonstrated that the deep learning-based de novo molecular design could efficiently accelerate the drug discovery process. The flourish of the de novo molecular generation methods and applications created a great demand for the visualization and functional profiling for the de novo generated molecules. The rising of publicly available chemogenomic databases lays good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification \& visualization, (2) chemical space, (3) scaffold analysis, (4) molecular alignment, (5) drugs mapping, and (6) target \& pathway. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target \& pathway information. The comprehensive annotated information could give users a clear picture of their de novo library and could guide the further selection of candidates for synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.},
- author = {Liu, Zhihong and Du, Jiewen and Liu, Bingdong and Cui, Zongbin and Fang, Jiansong and Xie, Liwei},
- doi = {10.21203/rs.3.rs-142605/v2},
- journal = {Research Square},
- keywords = {+RefPublic, {\textgreater}ChemicalToolbox},
- month = {August},
- note = {ISSN: 2693-5015
-Type: article},
- shorttitle = {{DenovoProfiling}},
- title = {{DenovoProfiling}: a webserver for de novo generated molecule library profiling},
- url = {https://www.researchsquare.com/article/rs-142605/v2},
- urldate = {2021-08-19},
- year = {2021}
-}
-
-@article{lodewijk_evolution_2020,
- abstract = {Summary.  Ever since the availability of genomes from Neanderthals, Denisovans and ancient humans, the field of evolutionary genomics has been searching for pro},
- author = {Lodewijk, Gerrald A. and Fernandes, Diana P. and Vretzakis, Iraklis and Savage, Jeanne E. and Jacobs, Frank M. J.},
- doi = {10.1093/molbev/msaa104},
- journal = {Molecular Biology and Evolution},
- keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {April},
- title = {Evolution of human brain size-associated {NOTCH2NL} genes proceeds towards reduced protein levels},
- url = {https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa104/5824797},
- urldate = {2020-05-22},
- year = {2020}
-}
-
-@article{lopez-delisle_pygenometracks_2020,
- abstract = {AbstractMotivation.  Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures r},
- author = {Lopez-Delisle, Lucille and Rabbani, Leily and Wolff, Joachim and Bhardwaj, Vivek and Backofen, Rolf and Grüning, Björn and Ramírez, Fidel and Manke, Thomas},
- doi = {10.1093/bioinformatics/btaa692},
- journal = {Bioinformatics},
- keywords = {+Galactic, +Tools, +Visualization, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- shorttitle = {{pyGenomeTracks}},
- title = {{pyGenomeTracks}: reproducible plots for multivariate genomic data sets},
- url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa692/5879987},
- urldate = {2020-08-20},
- year = {2020}
-}
-
-@article{lother_diabetes_2020,
- abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}h3{\textgreater}Background{\textless}/h3{\textgreater}{\textless}p{\textgreater}Diabetes mellitus is a worldwide epidemic that causes high mortality due to cardiovascular complications, in particular heart failure. Diabetes is associated with profound pathophysiological changes in the heart. The aim of this study was to investigate the impact of diabetes on gene expression and DNA methylation in cardiac cells.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and results{\textless}/h3{\textgreater}{\textless}p{\textgreater}Transcriptome analysis of heart tissue from mice with streptozotocin-induced diabetes revealed only 39 genes regulated, whereas cell type-specific analysis of the diabetic heart was more sensitive and more specific than heart tissue analysis and revealed a total of 3205 differentially regulated genes in five cell types. Whole genome DNA methylation analysis with basepair resolution of distinct cardiac cell types identified highly specific DNA methylation signatures of genic and regulatory regions. Interestingly, despite marked changes in gene expression, DNA methylation remained stable in streptozotocin-induced diabetes. Integrated analysis of cell type-specific gene expression enabled us to assign the particular contribution of single cell types to the pathophysiology of the diabetic heart. Finally, analysis of gene regulation revealed ligand-receptor pairs as potential mediators of heterocellular interaction in the diabetic heart, with fibroblasts and monocytes showing the highest degree of interaction.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusion{\textless}/h3{\textgreater}{\textless}p{\textgreater}In summary, cell type-specific analysis reveals differentially regulated gene programs that are associated with distinct biological processes in diabetes. Interestingly, despite these changes in gene expression, cell type-specific DNA methylation signatures of genic and regulatory regions remain stable in diabetes. Analysis of heterocellular interactions in the diabetic heart suggest that the interplay between fibroblasts and monocytes is of pivotal importance.{\textless}/p{\textgreater}},
- author = {Lother, Achim and Bondareva, Olga and Saadatmand, Ali R. and Pollmeier, Luisa and Härdtner, Carmen and Hilgendorf, Ingo and Weichenhan, Dieter and Eckstein, Volker and Plass, Christoph and Bode, Christoph and Backs, Johannes and Hein, Lutz and Gilsbach, Ralf},
- doi = {10.1016/j.yjmcc.2020.11.004},
- issn = {0022-2828, 1095-8584},
- journal = {Journal of Molecular and Cellular Cardiology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {English},
- month = {November},
- note = {Publisher: Elsevier},
- number = {0},
- pmid = {33197445},
- title = {Diabetes changes gene expression but not {DNA} methylation in cardiac cells},
- url = {https://www.jmmc-online.com/article/S0022-2828(20)30327-8/abstract},
- urldate = {2020-11-23},
- volume = {0},
- year = {2020}
-}
-
-@article{lother_endothelial_2019,
- author = {Lother, Achim and Deng, Lisa and Huck, Michael and Fürst, David and Kowalski, Jessica and Esser, Jennifer S. and Moser, Martin and Bode, Christoph and Hein, Lutz},
- doi = {10.1530/JOE-18-0494},
- issn = {0022-0795, 1479-6805},
- journal = {Journal of Endocrinology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en\_US},
- month = {January},
- number = {1},
- pages = {15--26},
- title = {Endothelial cell mineralocorticoid receptors oppose {VEGF}-induced gene expression and angiogenesis},
- url = {https://joe.bioscientifica.com/abstract/journals/joe/240/1/JOE-18-0494.xml},
- urldate = {2018-11-29},
- volume = {240},
- year = {2019}
-}
-
-@article{lucaci_rascl_2022,
- author = {Lucaci, Alexander G and Zehr, Jordan D and Shank, Stephen D and Bouvier, Dave and Mei, Han and Nekrutenko, Anton and Martin, Darren P and Pond, Sergei},
- journal = {bioRxiv},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {{RASCL}: {Rapid} {Assessment} {Of} {SARS}-{CoV}-2 {Clades} {Through} {Molecular} {Sequence} {Analysis}},
- year = {2022}
-}
-
-@article{luo_3d_2021,
- abstract = {Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque, and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. The human-specific loops are significantly enriched in enhancer-enhancer interactions, and the regulated genes show human-specific expression changes in the subplate, a transient zone of the developing brain critical for neural circuit formation and plasticity. Notably, many human-specific sequence changes are located in the human-specific TAD boundaries and loop anchors, which may generate new transcription factor binding sites and chromatin structures in human. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of brain development and evolution.},
- author = {Luo, Xin and Liu, Yuting and Dang, Dachang and Hu, Ting and Hou, Yingping and Meng, Xiaoyu and Zhang, Fengyun and Li, Tingting and Wang, Can and Li, Min and Wu, Haixu and Shen, Qiushuo and Hu, Yan and Zeng, Xuerui and He, Xiechao and Yan, Lanzhen and Zhang, Shihua and Li, Cheng and Su, Bing},
- doi = {10.1016/j.cell.2021.01.001},
- issn = {0092-8674},
- journal = {Cell},
- keywords = {+Methods, +UsePublic, 3D genome, {\textgreater}UseGalaxy.eu, EPHA7, TAD, brain, brain evolution, chromatin structure, corticogenesis, loop, macaque, subplate},
- language = {en},
- month = {February},
- number = {3},
- pages = {723--740.e21},
- title = {{3D} {Genome} of macaque fetal brain reveals evolutionary innovations during primate corticogenesis},
- url = {https://www.sciencedirect.com/science/article/pii/S0092867421000015},
- urldate = {2021-07-17},
- volume = {184},
- year = {2021}
-}
-
-@article{ma_somatostatin_2020,
- abstract = {Somatostatin is a neuropeptide and a key regulator of the growth axis. Six Sst encoding genes (sst1 to sst6) have been identified in teleost fish genomes but little is known about their function. The present study aimed at replicating the context of the inflammatory bowel disease (IBD) and clarifying the involvement of sst3 in the intestine innate defence barrier in zebrafish larvae. We first established a CRISP/Cas9 sst3 deficient line (MT) and analysed the morphological and transcriptomic response to 0.4\% dextran sulfate sodium (DSS). Alcian blue staining of larval sections 6 days post fertilization showed an increased in acidic mucins in the intestinal bulb and mid-intestine, with a much stronger response in the MT compared to wild type (WT). The transcriptomic analysis revealed that WT and MT shared enriched gene ontology (GO) terms and pathways linked to catabolism, chondrocyte development, innate immune system, xenobiotic metabolism and oxidative stress. In contrast, the WT specific response to DSS was enriched in GO terms and pathways linked to transcription and translation, various developmental processes, regulation of biosynthetic processes, apelin signalling and apoptosis while the MT specific response included terms and pathways linked to protein metabolism and catabolic processes, extracellular matrix – receptor interaction and proteasome and chondrocyte development. Overall, this study demonstrated that Sst3 deficiency impairs insulin growth factor and adipocytokine signalling exacerbating the inflammatory response to DSS.},
- author = {Ma, Jing and Chen, Jie and Louro, Bruno and Martins, Rute S. T. and Canario, Adelino V. M.},
- doi = {10.1016/j.aaf.2020.09.001},
- issn = {2468-550X},
- journal = {Aquaculture and Fisheries},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, IBD, Inflammation, RNA-Seq, Somatostatin 3, Zebrafish},
- language = {en},
- month = {September},
- title = {Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation},
- url = {https://www.sciencedirect.com/science/article/pii/S2468550X20301234},
- urldate = {2021-05-12},
- year = {2020}
-}
-
-@article{mack_regulation_2022,
- author = {Mack, Hildegard I. D. and Kremer, Jennifer and Albertini, Eva and Mack, Elisabeth K. M. and Jansen-Dürr, Pidder},
- doi = {10.1186/s12864-021-08176-y},
- journal = {BMC Genomics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/{DYRK1A} in {Caenorhabditis} elegans},
- url = {https://doi.org/10.1186/s12864-021-08176-y},
- volume = {23},
- year = {2022}
-}
-
-@article{macnee_simtext_2021,
- author = {Macnee, Marie and Pérez-Palma, Eduardo and Schumacher-Bass, Sarah and Dalton, Jarrod and Leu, Costin and Blankenberg, Daniel and Lal, Dennis},
- doi = {10.1093/bioinformatics/btab365},
- editor = {Wren, Jonathan},
- journal = {Bioinformatics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {May},
- note = {Publisher: Oxford University Press (OUP)},
- title = {{SimText}: a text mining framework for interactive analysis and visualization of similarities among biomedical entities},
- url = {https://doi.org/10.1093/bioinformatics/btab365},
- year = {2021}
-}
-
-@article{maier_freely_2021,
- abstract = {{\textless}p{\textgreater}The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.{\textless}/p{\textgreater}},
- author = {Maier, Wolfgang and Bray, Simon and Beek, Marius van den and Bouvier, Dave and Coraor, Nathaniel and Miladi, Milad and Singh, Babita and Argila, Jordi Rambla De and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren and Lonie, Andrew and Gruning, Bjorn and Pond, Sergei Kosakovsky and Nekrutenko, Anton},
- copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
- doi = {10.1101/2021.03.25.437046},
- journal = {bioRxiv},
- keywords = {+Education, +Galactic, +Methods, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2021.03.25.437046},
- title = {Freely accessible ready to use global infrastructure for {SARS}-{CoV}-2 monitoring},
- url = {https://www.biorxiv.org/content/10.1101/2021.03.25.437046v1},
- urldate = {2021-03-26},
- year = {2021}
-}
-
-@article{maier_ready--use_2021,
- author = {Maier, Wolfgang and Bray, Simon and van den Beek, Marius and Bouvier, Dave and Coraor, Nathan and Miladi, Milad and Singh, Babita and De Argila, Jordi Rambla and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren P. and Lonie, Andrew and Grüning, Björn and Kosakovsky Pond, Sergei L. and Nekrutenko, Anton},
- copyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc.},
- doi = {10.1038/s41587-021-01069-1},
- issn = {1546-1696},
- journal = {Nature Biotechnology},
- keywords = {+Galactic, +IsGalaxy, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {September},
- note = {Bandiera\_abtest: a
-Cg\_type: Nature Research Journals
-Primary\_atype: Correspondence
-Publisher: Nature Publishing Group
-Subject\_term: Genomic analysis;SARS-CoV-2
-Subject\_term\_id: genomic-analysis;sars-cov-2},
- pages = {1--2},
- title = {Ready-to-use public infrastructure for global {SARS}-{CoV}-2 monitoring},
- url = {https://www.nature.com/articles/s41587-021-01069-1},
- urldate = {2021-10-01},
- year = {2021}
-}
-
-@article{marisaldi_novo_2021,
- abstract = {In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length ({\textgreater}80\% coverage), with an Ex90N50 of 3061 bp and 76\% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1\% of tuna transcripts were included in orthogroups with other species and 5.1\% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.},
- author = {Marisaldi, Luca and Basili, Danilo and Gioacchini, Giorgia and Canapa, Adriana and Carnevali, Oliana},
- doi = {10.1016/j.margen.2020.100834},
- issn = {1874-7787},
- journal = {Marine Genomics},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Larval transcriptome, Transcriptomics, Tuna larvae},
- language = {en},
- month = {August},
- pages = {100834},
- title = {De novo transcriptome assembly, functional annotation and characterization of the {Atlantic} bluefin tuna ({Thunnus} thynnus) larval stage},
- url = {https://www.sciencedirect.com/science/article/pii/S1874778720300957},
- urldate = {2021-08-19},
- volume = {58},
- year = {2021}
-}
-
-@article{martin_selection_2022,
- author = {Martin, Darren P and Lytras, Spyro and Lucaci, Alexander G and Maier, Wolfgang and Gruning, Bjorn and Shank, Stephen D and Weaver, Steven and MacLean, Oscar S and Orton, Richard J and Lemey, Philippe and {others}},
- journal = {bioRxiv},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Selection analysis identifies unusual clustered mutational changes in {Omicron} lineage {BA}. 1 that likely impact {Spike} function},
- year = {2022}
-}
-
-@article{martinez-fabregas_cdk8_2020,
- abstract = {Cytokines are highly pleiotropic ligands that regulate the immune response. Here, using interleukin-6 (IL-6) as a model system, we perform detailed phosphoproteomic and transcriptomic studies in human CD4+ T helper 1 (Th-1) cells to address the molecular bases defining cytokine functional pleiotropy. We identify CDK8 as a negative regulator of STAT3 transcriptional activities, which interacts with STAT3 upon IL-6 stimulation. Inhibition of CDK8 activity, using specific small molecule inhibitors, reduces the IL-6-induced phosphoproteome by 23\% in Th-1 cells, including STAT3 S727 phosphorylation. STAT3 binding to target DNA sites in the genome is increased upon CDK8 inhibition, which results in a concomitant increase in STAT3-mediated transcriptional activity. Importantly, inhibition of CDK8 activity under Th-17 polarizing conditions results in an enhancement of Th-17 differentiation. Our results support a model where CDK8 regulates STAT3 transcriptional processivity by modulation of its gene loci resident time, critically contributing to diversification of IL-6 responses.},
- author = {Martinez-Fabregas, Jonathan and Wang, Luopin and Pohler, Elizabeth and Cozzani, Adeline and Wilmes, Stephan and Kazemian, Majid and Mitra, Suman and Moraga, Ignacio},
- doi = {10.1016/j.celrep.2020.108545},
- issn = {2211-1247},
- journal = {Cell Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- number = {12},
- pages = {108545},
- title = {{CDK8} {Fine}-{Tunes} {IL}-6 {Transcriptional} {Activities} by {Limiting} {STAT3} {Resident} {Time} at the {Gene} {Loci}},
- url = {https://www.sciencedirect.com/science/article/pii/S2211124720315345},
- urldate = {2021-07-21},
- volume = {33},
- year = {2020}
-}
-
-@article{martins_rodrigues_dataplant_2021,
- author = {Martins Rodrigues, Cristina and von Suchodoletz, Dirk and Mühlhaus, Timo and Krüger, Jens and Usadel, Björn},
- copyright = {Creative Commons Attribution 4.0 International},
- doi = {10.17192/BFDM.2021.2.8335},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- language = {de},
- note = {Publisher: Philipps-Universität Marburg},
- title = {{DataPLANT} – {Ein} {NFDI}-{Konsortium} der {Pflanzen}-{Grundlagenforschung}},
- url = {https://bausteine-fdm.de/article/view/8335},
- year = {2021}
-}
-
-@article{marzoli_next_2020,
- abstract = {The predator Asian hornet (Vespa velutina) represents one of the major threats to honeybee survival. Viral spillover from bee to wasp has been supposed in several studies, and this work aims to identify and study the virome of both insect species living simultaneously in the same foraging area. Transcriptomic analysis was performed on V. velutina and Apis mellifera samples, and replicative form of detected viruses was carried out by strand-specific RT-PCR. Overall, 6 and 9 different viral types were reported in V. velutina and A. mellifera, respectively, and five of these viruses were recorded in both hosts. Varroa destructor virus-1 and Cripavirus NB-1/2011/HUN (now classified as Triato-like virus) were the most represented viruses detected in both hosts, also in replicative form. In this investigation, Triato-like virus, as well as Aphis gossypii virus and Nora virus, was detected for the first time in honeybees. Concerning V. velutina, we report for the first time the recently detected honeybee La Jolla virus. A general high homology rate between genomes of shared viruses between V. velutina and A. mellifera suggests the efficient transmission of the virus from bee to wasp. In conclusion, our findings highlight the presence of several known and newly reported RNA viruses infecting A. mellifera and V. velutina. This confirms the environment role as an important source of infection and indicates the possibility of spillover from prey to predator.},
- author = {Marzoli, Filippo and Forzan, Mario and Bortolotti, Laura and Pacini, Maria Irene and Rodríguez‐Flores, María Shantal and Felicioli, Antonio and Mazzei, Maurizio},
- copyright = {© 2020 Wiley‐VCH GmbH},
- doi = {https://doi.org/10.1111/tbed.13878},
- issn = {1865-1682},
- journal = {Transboundary and Emerging Diseases},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Vespidae, honey bee viruses, next-generation sequencing, virology},
- language = {en},
- month = {October},
- note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tbed.13878},
- number = {n/a},
- title = {Next generation sequencing study on {RNA} viruses of {Vespa} velutina and {Apis} mellifera sharing the same foraging area},
- url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tbed.13878},
- urldate = {2021-04-14},
- volume = {n/a},
- year = {2020}
-}
-
-@article{mauer_genomics_2021,
- author = {Mauer, Katharina M. and Schmidt, Hanno and Dittrich, Marco and Fröbius, Andreas C. and Hellmann, Sören Lukas and Zischler, Hans and Hankeln, Thomas and Herlyn, Holger},
- doi = {10.1186/s12864-021-07857-y},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Genomics and transcriptomics of epizoic {Seisonidea} ({Rotifera}, syn. {Syndermata}) reveal strain formation and gradual gene loss with growing ties to the host},
- url = {https://doi.org/10.1186/s12864-021-07857-y},
- volume = {22},
- year = {2021}
-}
-
-@article{mcdonald_ultraviolet_2022,
- author = {McDonald, Marisa S. and Palecanda, Sitara and Cohen, Jonathan H. and Porter, Megan L.},
- doi = {10.1242/jeb.243256},
- journal = {Journal of Experimental Biology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: The Company of Biologists},
- title = {Ultraviolet vision in larval {Neogonodactylus} oerstedii},
- url = {https://doi.org/10.1242/jeb.243256},
- year = {2022}
-}
-
-@article{mcerlean_epigenetic_2020,
- abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}p{\textgreater}Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, the epigenetics of AMs development and function in IPF are limited. Here, we characterised the DNA-methylation (DNAm) profile of AMs from IPF (n=30) and healthy (n=14) donors. Our analysis revealed epigenetic heterogeneity was a key characteristic of IPF AMs. DNAm ‘clock’ analysis indicated epigenetic alterations in IPF-AMs was not associated with accelerated ageing. In differential DNAm analysis, we identified numerous differentially methylated positions (DMPs, n=11) and regions (DMRs, n=49) between healthy and IPF AMs respectively. DMPs and DMRs encompassed genes involved in lipid (\textit{LPCAT1}) and glucose (\textit{PFKB3}) metabolism and importantly, DNAm status was associated with disease severity in IPF. Collectively, our data identify that profound changes in the epigenome underpin the development and function of AMs in the IPF lung.{\textless}/p{\textgreater}},
- author = {McErlean, Peter and Bell, Christopher G. and Hewitt, Richard J. and Busharat, Zabreen and Ogger, Patricia P. and Ghai, Poonam and Albers, Gesa and Kingston, Shaun and Molyneaux, Philip L. and Beck, Stephan and Lloyd, Clare M. and Maher, Toby M. and Byrne, Adam J.},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/2020.12.04.410191},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.12.04.410191},
- title = {Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis},
- url = {https://www.biorxiv.org/content/10.1101/2020.12.04.410191v1},
- urldate = {2021-02-11},
- year = {2020}
-}
-
-@article{mcgill_sex-specific_2020,
- author = {McGill, Mahalia M. and Sabikunnahar, Bristy and Fang, Qian and Teuscher, Cory and Krementsov, Dimitry N.},
- doi = {10.1016/j.jneuroim.2020.577209},
- issn = {0165-5728},
- journal = {Journal of Neuroimmunology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- pages = {577209},
- title = {The sex-specific role of p38 {MAP} kinase in {CNS} autoimmunity is regulated by estrogen receptor alpha},
- url = {http://www.sciencedirect.com/science/article/pii/S0165572820300333},
- urldate = {2020-03-30},
- volume = {342},
- year = {2020}
-}
-
-@article{mcgowan_multi-omics_2020,
- abstract = {AbstractBackground.  Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences a},
- author = {McGowan, Thomas and Johnson, James E. and Kumar, Praveen and Sajulga, Ray and Mehta, Subina and Jagtap, Pratik D. and Griffin, Timothy J.},
- doi = {10.1093/gigascience/giaa025},
- journal = {GigaScience},
- keywords = {+Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {April},
- note = {Publisher: Oxford Academic},
- number = {4},
- shorttitle = {Multi-omics {Visualization} {Platform}},
- title = {Multi-omics {Visualization} {Platform}: {An} extensible {Galaxy} plug-in for multi-omics data visualization and exploration},
- url = {https://academic.oup.com/gigascience/article/9/4/giaa025/5813097},
- urldate = {2020-08-16},
- volume = {9},
- year = {2020}
-}
-
-@article{mehta_asaim-mt_2021,
- abstract = {The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.},
- author = {Mehta, Subina and Crane, Marie and Leith, Emma and Batut, Bérénice and Hiltemann, Saskia and Arntzen, Magnus Ø and Kunath, Benoit J. and Delogu, Francesco and Sajulga, Ray and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.},
- doi = {10.12688/f1000research.28608.1},
- issn = {2046-1402},
- journal = {F1000Research},
- keywords = {+Education, +Galactic, +IsGalaxy, +Tools, {\textgreater}ASaiM, {\textgreater}Metagenomics EU},
- language = {en},
- month = {February},
- pages = {103},
- shorttitle = {{ASaiM}-{MT}},
- title = {{ASaiM}-{MT}: a validated and optimized {ASaiM} workflow for metatranscriptomics analysis within {Galaxy} framework},
- url = {https://f1000research.com/articles/10-103/v1},
- urldate = {2021-02-12},
- volume = {10},
- year = {2021}
-}
-
-@article{mehta_precursor_2020,
- abstract = {For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and multi-omics studies such as metaproteomics (analyzing taxon-specific microbial peptides) and proteogenomics (analyzing non-canonical sequences). Bioinformatics workflows accessible via the Galaxy platform have proven useful for analysis of such complex multi-omic studies. However, workflows within the Galaxy platform have lacked well-tested LFQ tools. In this study, we have evaluated moFF and FlashLFQ, two open-source LFQ tools, and implemented them within the Galaxy platform to offer access and use via established workflows. Through rigorous testing and communication with the tool developers, we have optimized the performance of each tool. Software features evaluated include: (a) match-between-runs (MBR); (b) using multiple file-formats as input for improved quantification; (c) use of containers and/or conda packages; (d) parameters needed for analyzing large datasets; and (e) optimization and validation of software performance. This work establishes a process for software implementation, optimization, and validation, and offers access to two robust software tools for LFQ-based analysis within the Galaxy platform.},
- author = {Mehta, Subina and Easterly, Caleb W. and Sajulga, Ray and Millikin, Robert J. and Argentini, Andrea and Eguinoa, Ignacio and Martens, Lennart and Shortreed, Michael R. and Smith, Lloyd M. and McGowan, Thomas and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/proteomes8030015},
- journal = {Proteomes},
- keywords = {+Galactic, +Tools, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, galaxy framework, label-free quantification, proteomics, workflows},
- language = {en},
- month = {September},
- note = {Number: 3
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {3},
- pages = {15},
- title = {Precursor {Intensity}-{Based} {Label}-{Free} {Quantification} {Software} {Tools} for {Proteomic} and {Multi}-{Omic} {Analysis} within the {Galaxy} {Platform}},
- url = {https://www.mdpi.com/2227-7382/8/3/15},
- urldate = {2021-05-04},
- volume = {8},
- year = {2020}
-}
-
-@article{mehta_updates_2021,
- abstract = {metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ (“metatranscriptomics to metaQuantome”), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.},
- author = {Mehta, Subina and Kumar, Praveen and Crane, Marie and Johnson, James E. and Sajulga, Ray and Nguyen, Dinh Duy An and McGowan, Thomas and Arntzen, Magnus Ø. and Griffin, Timothy J. and Jagtap, Pratik D.},
- doi = {10.1021/acs.jproteome.0c00960},
- issn = {1535-3893},
- journal = {Journal of Proteome Research},
- keywords = {+Education, +IsGalaxy, +Methods, +RefPublic, +Stellar, +Tools, +UsePublic, {\textgreater}ASaiM, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: American Chemical Society},
- title = {Updates on {metaQuantome} {Software} for {Quantitative} {Metaproteomics}},
- url = {https://doi.org/10.1021/acs.jproteome.0c00960},
- urldate = {2021-03-09},
- year = {2021}
-}
-
-@article{miao_putative_2020,
- abstract = {We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The feature genes, which are differentially expressed in the particular cell group, jointly discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterised by the feature genes as markers. To benchmark this approach, we use expert-annotated scRNA-seq datasets from a range of experiments, as well as comparing to existing cell annotation methods, which are all based on a pre-existing reference. We show that our method automatically identifies the 'ground truth' cell assignments with high accuracy. Moreover, our method, Single Cell Clustering Assessment Framework (SCCAF) predicts new putative biologically meaningful cell-states in published data on haematopoiesis and the human cortex. SCCAF is available as an open-source software package on GitHub (https://github.com/SCCAF/sccaf) and as a Python package index and has also been implemented as a Galaxy tool in the Human Cell Atlas.},
- author = {Miao, Zhichao and Moreno, Pablo and Huang, Ni and Papatheodorou, Irene and Brazma, Alvis and Teichmann, Sarah A.},
- journal = {arXiv},
- keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods},
- month = {April},
- note = {arXiv: 2004.09847
-version: 1},
- title = {Putative cell type discovery from single-cell gene expression data},
- url = {http://arxiv.org/abs/2004.09847},
- urldate = {2020-05-28},
- year = {2020}
-}
-
-@article{migur_temperature-regulated_2021,
- author = {Migur, Anzhela and Heyl, Florian and Fuss, Janina and Srikumar, Afshan and Huettel, Bruno and Steglich, Claudia and Prakash, Jogadhenu S. S. and Reinhardt, Richard and Backofen, Rolf and Owttrim, George W. and Hess, Wolfgang R.},
- doi = {10.1093/jxb/erab416},
- editor = {Sharwood, Robert},
- journal = {Journal of Experimental Botany},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Oxford University Press (OUP)},
- title = {The temperature-regulated {DEAD}-box {RNA} helicase {CrhR} interactome: autoregulation and photosynthesis-related transcripts},
- url = {https://doi.org/10.1093/jxb/erab416},
- year = {2021}
-}
-
-@article{mootapally_sediment_2021,
- abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.},
- author = {Mootapally, Chandrashekar and Mahajan, Mayur S. and Nathani, Neelam M.},
- doi = {10.1007/s00248-020-01587-6},
- issn = {1432-184X},
- journal = {Microbial Ecology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- number = {2},
- pages = {540--548},
- shorttitle = {Sediment {Plasmidome} of the {Gulfs} of {Kathiawar} {Peninsula} and {Arabian} {Sea}},
- title = {Sediment {Plasmidome} of the {Gulfs} of {Kathiawar} {Peninsula} and {Arabian} {Sea}: {Insights} {Gained} from {Metagenomics} {Data}},
- url = {https://doi.org/10.1007/s00248-020-01587-6},
- urldate = {2021-05-12},
- volume = {81},
- year = {2021}
-}
-
-@article{morandi_evolutionary_2020,
- abstract = {Background: Ultra-conserved non-coding elements (UCNEs) are genomic sequences that exhibit \> 95\% sequence identity between humans, mammals, birds, reptiles, and fish. Recent findings reported their functional role in cancer. The aim of this study was to evaluate the DNA methylation modifications of UNCEs in squamous cell carcinoma (SCC) from different mammal species. Methods: Fifty SCCs from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger, and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite next generation sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, and uc.328). Results: 57/59 CpGs were significantly different according to the Kruskal\–Wallis test (p \< 0.05) comparing normal samples with SCC. A common DNA hypermethylation pattern was observed in SCCs from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC. Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.},
- author = {Morandi, Luca and Sabattini, Silvia and Renzi, Andrea and Rigillo, Antonella and Bettini, Giuliano and Dervas, Eva and Schauer, Alexandria and Morandi, Marco and Gissi, Davide B. and Tarsitano, Achille and Evangelisti, Stefania and Tonon, Caterina},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/cells9092092},
- journal = {Cells},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, DNA methylation, bisulfite sequencing, evolutionary epigenetics, squamous cell carcinoma, ultra-conserved non-coding elements},
- language = {en},
- month = {September},
- note = {Number: 9
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {9},
- pages = {2092},
- title = {An {Evolutionary} {Cancer} {Epigenetic} {Approach} {Revealed} {DNA} {Hypermethylation} of {Ultra}-{Conserved} {Non}-{Coding} {Elements} in {Squamous} {Cell} {Carcinoma} of {Different} {Mammalian} {Species}},
- url = {https://www.mdpi.com/2073-4409/9/9/2092},
- urldate = {2020-12-29},
- volume = {9},
- year = {2020}
-}
-
-@article{moreno_expression_2021,
- author = {Moreno, Pablo and Fexova, Silvie and George, Nancy and Manning, Jonathan R. and Miao, Zhichiao and Mohammed, Suhaib and Muñoz-Pomer, Alfonso and Fullgrabe, Anja and Bi, Yalan and Bush, Natassja and Iqbal, Haider and Kumbham, Upendra and Solovyev, Andrey and Zhao, Lingyun and Prakash, Ananth and García-Seisdedos, David and Kundu, Deepti J. and Wang, Shengbo and Walzer, Mathias and Clarke, Laura and Osumi-Sutherland, David and Tello-Ruiz, Marcela Karey and Kumari, Sunita and Ware, Doreen and Eliasova, Jana and Arends, Mark J. and Nawijn, Martijn C. and Meyer, Kerstin and Burdett, Tony and Marioni, John and Teichmann, Sarah and Vizcaíno, Juan Antonio and Brazma, Alvis and Papatheodorou, Irene},
- doi = {10.1093/nar/gkab1030},
- journal = {Nucleic Acids Research},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {November},
- note = {Publisher: Oxford University Press (OUP)},
- number = {D1},
- pages = {D129--D140},
- title = {Expression {Atlas} update: gene and protein expression in multiple species},
- url = {https://doi.org/10.1093/nar/gkab1030},
- volume = {50},
- year = {2021}
-}
-
-@article{moreno_user-friendly_2021,
- author = {Moreno, Pablo and Huang, Ni and Manning, Jonathan R. and Mohammed, Suhaib and Solovyev, Andrey and Polanski, Krzysztof and Bacon, Wendi and Chazarra, Ruben and Talavera-López, Carlos and Doyle, Maria A. and Marnier, Guilhem and Grüning, Björn and Rasche, Helena and George, Nancy and Fexova, Silvie Korena and Alibi, Mohamed and Miao, Zhichao and Perez-Riverol, Yasset and Haeussler, Maximilian and Brazma, Alvis and Teichmann, Sarah and Meyer, Kerstin B. and Papatheodorou, Irene},
- doi = {10.1038/s41592-021-01102-w},
- journal = {Nature Methods},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Springer Science and Business Media LLC},
- title = {User-friendly, scalable tools and workflows for single-cell {RNA}-seq analysis},
- url = {https://doi.org/10.1038/s41592-021-01102-w},
- year = {2021}
-}
-
-@article{morsli_direct_2021,
- abstract = {The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81\% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.},
- author = {Morsli, Madjid and Zandotti, Christine and Morand, Aurelie and Colson, Philippe and Drancourt, Michel},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/pathogens10050610},
- journal = {Pathogens},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Echovirus 12, cerebrospinal fluid, enterovirus meningitis, metagenomic next-generation sequencing, whole genome sequencing},
- language = {en},
- month = {May},
- note = {Number: 5
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {5},
- pages = {610},
- title = {Direct {Diagnosis} of {Echovirus} 12 {Meningitis} {Using} {Metagenomic} {Next} {Generation} {Sequencing}},
- url = {https://www.mdpi.com/2076-0817/10/5/610},
- urldate = {2021-08-23},
- volume = {10},
- year = {2021}
-}
-
-@article{muller-ruch_glp_2020,
- abstract = {In biomedical research, enormous progress is being made and new candidates for putative medicinal products emerge. However, most published preclinical data are not conducted according to the standard Good Laboratory Practice (GLP). GLP is mandatory for preclinical analysis of Advanced Therapy Medicinal Products (ATMP) and thereby a prerequisite for planning and conduction of clinical trials. Not inconsiderable numbers of clinical trials are terminated earlier or fail – do inadequate testing strategies or missing specialized assays during the preclinical development contribute to this severe complex of problems? Unfortunately, there is also a lack of access to GLP testing results and OECD (Organisation for Economic Co-operation and Development) GLP guidelines are not yet adjusted to ATMP specialties. Ultimately, GLP offers possibilities to generate reliable and reproducible data. Therefore, this review elucidates different GLP aspects in drug development, speculates on reasons of putative low GLP acceptance in the scientific community and mentions solution proposals.},
- author = {Müller-Ruch, Ulrike and Skorska, Anna and Lemcke, Heiko and Steinhoff, Gustav and David, Robert},
- doi = {10.1016/j.addr.2020.04.003},
- issn = {0169-409X},
- journal = {Advanced Drug Delivery Reviews},
- keywords = {+RefPublic, {\textgreater}RNA Workbench},
- language = {en},
- month = {April},
- shorttitle = {{GLP}},
- title = {{GLP}: {A} requirement in cell therapies - perspectives for the cardiovascular field},
- url = {http://www.sciencedirect.com/science/article/pii/S0169409X20300235},
- urldate = {2020-05-26},
- year = {2020}
-}
-
-@article{muller_snp_2020,
- abstract = {Background
-Diet induced weight loss represents an intervention for obesity to prevent associated diseases. However there is considerable inter-individual variation. Single nucleotide polymorphisms (SNPs) and plasma miRNA might be contributing factors. We therefore hypothesized that changes in the miRNA pattern during weight loss depend on the SNP genotype.
-Methods
-Plasma miRNA profiles from 12 patients were determined before and after a three month weight loss intervention by Illumina sequencing. 46 further patients were analyzed by qPCR. SNP genotypes were determined on the Sequenom iPLEX platform.
-Results
-Samples before and after weight loss were analyzed by miRNA-seq and delta miRNA levels ranked according to p-value. Levels of miRNAs 25, 93 and 106 that are expressed from a common genomic cluster were reduced after weight loss. Those results were substantiated in a qPCR analysis of 46 additional patients. This is in accordance with mouse data showing a functional involvement of this cluster in obesity. Correlation of the changes in miRNA abundance with SNP genotypes revealed a statistical association of all three miRNAs with known obesity susceptibility SNPs.
-Conclusion
-Diet induced weight loss leads to SNP dependent modulation of miRNAs from the miR 25/93/106 gene cluster in humans.},
- author = {Müller, Stephanie and Wallner, Stefan and Schmitz, Gerd and Loew, Thomas and Stempfl, Thomas and Möhle, Christoph and Strack, Christina and Sag, Sabine and Baessler, Andrea and Fischer, Marcus},
- doi = {10.1016/j.gene.2020.144787},
- issn = {0378-1119},
- journal = {Gene},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Next generation sequencing, Obesity, Single nucleotide polymorphism, miRNA},
- language = {en},
- month = {August},
- pages = {144787},
- title = {{SNP} dependent modulation of circulating {miRNAs} from the {miR25}/93/106 cluster in patients undergoing weight loss},
- url = {http://www.sciencedirect.com/science/article/pii/S037811192030456X},
- urldate = {2020-05-28},
- volume = {753},
- year = {2020}
-}
-
-@article{musmeci_draft_2021,
- author = {Musmeci, Eliana and Candeliere, Francesco and Amaretti, Alberto and Rossi, Maddalena and Raimondi, Stefano},
- doi = {10.1128/mra.00642-21},
- editor = {Rasko, David},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: American Society for Microbiology},
- number = {32},
- title = {Draft {Genome} {Sequence} of the {Mucin} {Degrader} {Clostridium} tertium {WC0709}},
- url = {https://doi.org/10.1128/mra.00642-21},
- volume = {10},
- year = {2021}
-}
-
-@article{nagy_draft_2021,
- author = {Nagy, Nikoletta A. and Rácz, Rita and Rimington, Oliver and Póliska, Szilárd and Orozco-terWengel, Pablo and Bruford, Michael W. and Barta, Zoltán},
- doi = {10.1186/s12864-021-07627-w},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Draft genome of a biparental beetle species, {Lethrus} apterus},
- url = {https://doi.org/10.1186/s12864-021-07627-w},
- volume = {22},
- year = {2021}
-}
-
-@article{nagy_draft_2021,
- abstract = {The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring.},
- author = {Nagy, Nikoletta A. and Rácz, Rita and Rimington, Oliver and Póliska, Szilárd and Orozco-terWengel, Pablo and Bruford, Michael W. and Barta, Zoltán},
- doi = {10.1186/s12864-021-07627-w},
- issn = {1471-2164},
- journal = {BMC Genomics},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Coleoptera, Genome assembly, Geotrupidae, Parental behaviour},
- month = {April},
- number = {1},
- pages = {301},
- title = {Draft genome of a biparental beetle species, {Lethrus} apterus},
- url = {https://doi.org/10.1186/s12864-021-07627-w},
- urldate = {2021-08-24},
- volume = {22},
- year = {2021}
-}
-
-@article{naimi_direct_2021,
- abstract = {Epidemiologic evidence and animal studies implicate dietary emulsifiers in contributing to the increased prevalence of diseases associated with intestinal inflammation, including inflammatory bowel diseases and metabolic syndrome. Two synthetic emulsifiers in particular, carboxymethylcellulose and polysorbate 80, profoundly impact intestinal microbiota in a manner that promotes gut inflammation and associated disease states. In contrast, the extent to which other food additives with emulsifying properties might impact intestinal microbiota composition and function is not yet known.},
- author = {Naimi, Sabrine and Viennois, Emilie and Gewirtz, Andrew T. and Chassaing, Benoit},
- doi = {10.1186/s40168-020-00996-6},
- issn = {2049-2618},
- journal = {Microbiome},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- number = {1},
- pages = {66},
- title = {Direct impact of commonly used dietary emulsifiers on human gut microbiota},
- url = {https://doi.org/10.1186/s40168-020-00996-6},
- urldate = {2021-08-23},
- volume = {9},
- year = {2021}
-}
-
-@article{nekrutenko_biology_2018,
- abstract = {Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg; Biology needs evolutionary software tools: Let’s build them right, Molecular Bi},
- author = {Nekrutenko, Anton and Team, Galaxy and Goecks, Jeremy and Taylor, James and Blankenberg, Daniel},
- doi = {10.1093/molbev/msy084},
- journal = {Molecular Biology and Evolution},
- keywords = {+Galactic, +Project, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {April},
- shorttitle = {Biology needs evolutionary software tools},
- title = {Biology needs evolutionary software tools: {Let}’s build them right},
- url = {https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msy084/4983859},
- urldate = {2018-05-03},
- year = {2018}
-}
-
-@article{niemoller_bisulfite-free_2021,
- abstract = {Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single acute myeloid leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between cell lines based on the DNA methylation and genetic profiles.},
- author = {Niemöller, Christoph and Wehrle, Julius and Riba, Julian and Claus, Rainer and Renz, Nathalie and Rhein, Janika and Bleul, Sabine and Stosch, Juliane M. and Duyster, Justus and Plass, Christoph and Lutsik, Pavlo and Lipka, Daniel B. and Lübbert, Michael and Becker, Heiko},
- copyright = {2021 The Author(s)},
- doi = {10.1038/s42003-021-01661-w},
- issn = {2399-3642},
- journal = {Communications Biology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- note = {Bandiera\_abtest: a
-Cc\_license\_type: cc\_by
-Cg\_type: Nature Research Journals
-Number: 1
-Primary\_atype: Research
-Publisher: Nature Publishing Group
-Subject\_term: Acute myeloid leukaemia;Cancer epigenetics;Methylation analysis;Tumour heterogeneity;Whole genome amplification
-Subject\_term\_id: acute-myeloid-leukaemia;cancer-epigenetics;methylation-analysis;tumour-heterogeneity;whole-genome-amplification},
- number = {1},
- pages = {1--10},
- title = {Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction},
- url = {https://www.nature.com/articles/s42003-021-01661-w},
- urldate = {2021-07-21},
- volume = {4},
- year = {2021}
-}
-
-@article{nuhrenberg_impact_2022,
- author = {Nührenberg, Thomas G. and Stöckle, Jasmin and Marini, Federico and Zurek, Mark and Grüning, Björn A. and Benes, Vladimir and Hein, Lutz and Neumann, Franz-Josef and Stratz, Christian and Cederqvist, Marco and Hochholzer, Willibald},
- doi = {10.1371/journal.pone.0260222},
- editor = {James, Katherine},
- journal = {PLOS ONE},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: Public Library of Science (PLoS)},
- number = {1},
- pages = {e0260222},
- title = {Impact of high platelet turnover on the platelet transcriptome: {Results} from platelet {RNA}-sequencing in patients with sepsis},
- url = {https://doi.org/10.1371/journal.pone.0260222},
- volume = {17},
- year = {2022}
-}
-
-@article{nunez-sanchez_characterizing_2020,
- abstract = {An intestinal epithelium model able to produce mucus was developed to provide an environment suitable for testing the therapeutic activity of gut bacteriophages. We show that Enterococcus faecalis adheres more effectively in the presence of mucus, can invade the intestinal epithelia and is able to translocate after damaging tight junctions. Furthermore, Enterococcus phage vB\_EfaM\_A2 (a member of Herelleviridae that possesses virion associated immunoglobin domains) was found to translocate through the epithelium in the presence and absence of its host bacteria. Phage A2 protected eukaryotic cells by reducing mortality and maintaining the structure of the cell layer structure. We suggest the mammalian cell model utilized within this study as an adaptable in vitro model that can be employed to enable a better understanding of phage\–bacteria interactions and the protective impact of phage therapy relating to the intestinal epithelium.},
- author = {Núñez-Sánchez, María A. and Colom, Joan and Walsh, Lauren and Buttimer, Colin and Bolocan, Andrei Sorin and Pang, Rory and Gahan, Cormac G. M. and Hill, Colin},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/microorganisms8091374},
- journal = {Microorganisms},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Enterococcus faecalis, Herelleviridae, IBD, bacteriophage, intestinal model, phage therapy},
- language = {en},
- month = {September},
- note = {Number: 9
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {9},
- pages = {1374},
- title = {Characterizing {Phage}-{Host} {Interactions} in a {Simplified} {Human} {Intestinal} {Barrier} {Model}},
- url = {https://www.mdpi.com/2076-2607/8/9/1374},
- urldate = {2021-01-07},
- volume = {8},
- year = {2020}
-}
-
-@article{oeyen_sawfly_2020,
- abstract = {Abstract.  The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (},
- author = {Oeyen, Jan Philip and Baa-Puyoulet, Patrice and Benoit, Joshua B. and Beukeboom, Leo W. and Bornberg-Bauer, Erich and Buttstedt, Anja and Calevro, Federica and Cash, Elizabeth I. and Chao, Hsu and Charles, Hubert and Chen, Mei-Ju May and Childers, Christopher and Cridge, Andrew G. and Dearden, Peter and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Dolan, Amanda and Donath, Alexander and Dowling, Daniel and Dugan, Shannon and Duncan, Elizabeth and Elpidina, Elena N. and Friedrich, Markus and Geuverink, Elzemiek and Gibson, Joshua D. and Grath, Sonja and Grimmelikhuijzen, Cornelis J. P. and Große-Wilde, Ewald and Gudobba, Cameron and Han, Yi and Hansson, Bill S. and Hauser, Frank and Hughes, Daniel S. T. and Ioannidis, Panagiotis and Jacquin-Joly, Emmanuelle and Jennings, Emily C. and Jones, Jeffery W. and Klasberg, Steffen and Lee, Sandra L. and Lesný, Peter and Lovegrove, Mackenzie and Martin, Sebastian and Martynov, Alexander G. and Mayer, Christoph and Montagné, Nicolas and Moris, Victoria C. and Munoz-Torres, Monica and Murali, Shwetha Canchi and Muzny, Donna M. and Oppert, Brenda and Parisot, Nicolas and Pauli, Thomas and Peters, Ralph S. and Petersen, Malte and Pick, Christian and Persyn, Emma and Podsiadlowski, Lars and Poelchau, Monica F. and Provataris, Panagiotis and Qu, Jiaxin and Reijnders, Maarten J. M. F. and von Reumont, Björn Marcus and Rosendale, Andrew J. and Simao, Felipe A. and Skelly, John and Sotiropoulos, Alexandros G. and Stahl, Aaron L. and Sumitani, Megumi and Szuter, Elise M. and Tidswell, Olivia and Tsitlakidis, Evangelos and Vedder, Lucia and Waterhouse, Robert M. and Werren, John H. and Wilbrandt, Jeanne and Worley, Kim C. and Yamamoto, Daisuke S. and van de Zande, Louis and Zdobnov, Evgeny M. and Ziesmann, Tanja and Gibbs, Richard A. and Richards, Stephen and Hatakeyama, Masatsugu and Misof, Bernhard and Niehuis, Oliver},
- doi = {10.1093/gbe/evaa106},
- journal = {Genome Biology and Evolution},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {July},
- note = {Publisher: Oxford Academic},
- number = {7},
- pages = {1099--1188},
- title = {Sawfly {Genomes} {Reveal} {Evolutionary} {Acquisitions} {That} {Fostered} the {Mega}-{Radiation} of {Parasitoid} and {Eusocial} {Hymenoptera}},
- url = {https://academic.oup.com/gbe/article/12/7/1099/5842140},
- urldate = {2020-08-20},
- volume = {12},
- year = {2020}
-}
-
-@article{oselusi_cheminformatic_2021,
- author = {Oselusi, Samson Olaitan and Christoffels, Alan and Egieyeh, Samuel Ayodele},
- doi = {10.3390/molecules26133970},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: MDPI AG},
- number = {13},
- pages = {3970},
- title = {Cheminformatic {Characterization} of {Natural} {Antimicrobial} {Products} for the {Development} of {New} {Lead} {Compounds}},
- url = {https://doi.org/10.3390/molecules26133970},
- volume = {26},
- year = {2021}
-}
-
-@article{ostrovsky_using_2021,
- abstract = {Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density Basic Protocol 2: Calling peaks for ChIP-seq data Basic Protocol 3: Compare datasets using genomic coordinates Basic Protocol 4: Working with multiple alignments Basic Protocol 5: Single cell RNA-seq},
- author = {Ostrovsky, Alexander and Hillman‐Jackson, Jennifer and Bouvier, Dave and Clements, Dave and Afgan, Enis and Blankenberg, Daniel and Schatz, Michael C. and Nekrutenko, Anton and Taylor, James and Team, the Galaxy and Lariviere, Delphine},
- copyright = {© 2021 Wiley Periodicals LLC},
- doi = {https://doi.org/10.1002/cpz1.31},
- issn = {2691-1299},
- journal = {Current Protocols},
- keywords = {+Education, +Galactic, +HowTo, +IsGalaxy, +Project, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Galaxy, computational biology, web application},
- language = {en},
- note = {\_eprint: https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.31},
- number = {2},
- pages = {e31},
- title = {Using {Galaxy} to {Perform} {Large}-{Scale} {Interactive} {Data} {Analyses}—{An} {Update}},
- url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.31},
- urldate = {2021-02-15},
- volume = {1},
- year = {2021}
-}
-
-@article{owen_rna-sequencing_2019,
- abstract = {High-throughput, massively parallel sequence analysis has revolutionized the way that researchers design and execute scientific investigations. Vast amounts of sequence data can be generated in short periods of time. Regarding ophthalmology and vision research, extensive interrogation of patient samples for underlying causative DNA mutations has resulted in the discovery of many new genes relevant to eye disease. However, such analysis remains functionally limited. RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification. RNA-sequencing has the potential to advance our understanding of eye development and disease; it can reveal new candidates to improve our molecular diagnosis rates and highlight therapeutic targets for intervention. But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design. We review the key steps involved in RNA-sequencing experimental design and the downstream bioinformatic pipelines used for differential gene expression. We provide guidance on the application of RNAsequencing to ophthalmology and sources of open-access eye-related data sets.},
- author = {Owen, Nicholas and Moosajee, Mariya},
- doi = {10.1177/2515841419835460},
- issn = {2515-8414, 2515-8414},
- journal = {Therapeutic Advances in Ophthalmology},
- keywords = {+RefPublic, +Reproducibility, {\textgreater}RNA Workbench},
- language = {en},
- month = {January},
- pages = {251584141983546},
- shorttitle = {{RNA}-sequencing in ophthalmology research},
- title = {{RNA}-sequencing in ophthalmology research: considerations for experimental design and analysis},
- url = {http://journals.sagepub.com/doi/10.1177/2515841419835460},
- urldate = {2019-03-23},
- volume = {11},
- year = {2019}
-}
-
-@article{page-karjian_fibropapillomatosis_2021,
- author = {Page-Karjian, Annie and Whitmore, Liam and Stacy, Brian A. and Perrault, Justin R. and Farrell, Jessica A. and Shaver, Donna J. and Walker, J. Shelby and Frandsen, Hilary R. and Rantonen, Elina and Harms, Craig A. and Norton, Terry M. and Innis, Charles and Yetsko, Kelsey and Duffy, David J.},
- doi = {10.3390/ani11113076},
- journal = {Animals},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {October},
- note = {Publisher: MDPI AG},
- number = {11},
- pages = {3076},
- title = {Fibropapillomatosis and {Chelonid} {Alphaherpesvirus} 5 {Infection} in {Kemp}'s {Ridley} {Sea} {Turtles} ({Lepidochelys} kempii)},
- url = {https://doi.org/10.3390/ani11113076},
- volume = {11},
- year = {2021}
-}
-
-@article{pallares-vega_temperature_2021,
- author = {Pallares-Vega, Rebeca and Macedo, Gonçalo and Brouwer, Michael S. M. and Leal, Lucia Hernandez and Maas, Peter van der and Loosdrecht, Mark C. M. van and Weissbrodt, David G. and Heederik, Dick and Mevius, Dik and Schmitt, Heike},
- doi = {10.3389/fmicb.2021.656250},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Frontiers Media SA},
- title = {Temperature and {Nutrient} {Limitations} {Decrease} {Transfer} of {Conjugative} {IncP}-1 {Plasmid} {pKJK5} to {Wild} {Escherichia} coli {Strains}},
- url = {https://doi.org/10.3389/fmicb.2021.656250},
- volume = {12},
- year = {2021}
-}
-
-@article{papatheodorou_expression_2019,
- author = {Papatheodorou, Irene and Moreno, Pablo and Manning, Jonathan and Fuentes, Alfonso Muñoz-Pomer and George, Nancy and Fexova, Silvie and Fonseca, Nuno A. and Füllgrabe, Anja and Green, Matthew and Huang, Ni and Huerta, Laura and Iqbal, Haider and Jianu, Monica and Mohammed, Suhaib and Zhao, Lingyun and Jarnuczak, Andrew F. and Jupp, Simon and Marioni, John and Meyer, Kerstin and Petryszak, Robert and Medina, Cesar Augusto Prada and Talavera-López, Carlos and Teichmann, Sarah and Vizcaino, Juan Antonio and Brazma, Alvis},
- doi = {10.1093/nar/gkz947},
- journal = {Nucleic Acids Research},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {October},
- note = {Publisher: Oxford University Press (OUP)},
- title = {Expression {Atlas} update: from tissues to single cells},
- url = {https://doi.org/10.1093/nar/gkz947},
- year = {2019}
-}
-
-@article{parenti_mau2_2020,
- abstract = {The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations in NIPBL account for most cases of the rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report a MAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus. Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable for normal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fatal outcome of an out-of-frame single nucleotide duplication in NIPBL, engineered in two different cell lines, alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interact with MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protective against out-of-frame mutations that is potentially relevant for other genetic conditions.},
- author = {Parenti, Ilaria and Diab, Farah and Gil, Sara Ruiz and Mulugeta, Eskeatnaf and Casa, Valentina and Berutti, Riccardo and Brouwer, Rutger W. W. and Dupé, Valerie and Eckhold, Juliane and Graf, Elisabeth and Puisac, Beatriz and Ramos, Feliciano and Schwarzmayr, Thomas and Gines, Macarena Moronta and van Staveren, Thomas and van IJcken, Wilfred F. J. and Strom, Tim M. and Pié, Juan and Watrin, Erwan and Kaiser, Frank J. and Wendt, Kerstin S.},
- doi = {10.1016/j.celrep.2020.107647},
- issn = {2211-1247},
- journal = {Cell Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, CRISPR-Cas9, ChIP sequencing, Cornelia de Lange syndrome, MAU2, NIPBL, cohesin, cohesinopathy, rescue mechanism, transcriptomopathy},
- language = {en},
- month = {May},
- number = {7},
- pages = {107647},
- title = {{MAU2} and {NIPBL} {Variants} {Impair} the {Heterodimerization} of the {Cohesin} {Loader} {Subunits} and {Cause} {Cornelia} de {Lange} {Syndrome}},
- url = {http://www.sciencedirect.com/science/article/pii/S2211124720306008},
- urldate = {2020-08-19},
- volume = {31},
- year = {2020}
-}
-
-@article{pelletier_standardized_2021,
- author = {Pelletier, Dominique and Roos, David and Bouchoucha, Marc and Schohn, Thomas and Roman, William and Gonson, Charles and Bockel, Thomas and Carpentier, Liliane and Preuss, Bastien and Powell, Abigail and Garcia, Jessica and Gaboriau, Matthias and Cadé, Florent and Royaux, Coline and Bras, Yvan Le and Reecht, Yves},
- doi = {10.3389/fmars.2021.689280},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Frontiers Media SA},
- title = {A {Standardized} {Workflow} {Based} on the {STAVIRO} {Unbaited} {Underwater} {Video} {System} for {Monitoring} {Fish} and {Habitat} {Essential} {Biodiversity} {Variables} in {Coastal} {Areas}},
- url = {https://doi.org/10.3389/fmars.2021.689280},
- volume = {8},
- year = {2021}
-}
-
-@article{perez-schindler_discovery_2021,
- author = {Pérez-Schindler, Joaquín and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Handschin, Christoph},
- doi = {10.1101/2021.03.24.436772},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Discovery of lipotoxicity-sensitive transcription factors in non-alcoholic steatohepatitis},
- url = {https://doi.org/10.1101/2021.03.24.436772},
- year = {2021}
-}
-
-@article{perez-schindler_rna-bound_2021,
- author = {Pérez-Schindler, Joaquín and Kohl, Bastian and Schneider-Heieck, Konstantin and Leuchtmann, Aurel B. and Henríquez-Olguín, Carlos and Adak, Volkan and Maier, Geraldine and Delezie, Julien and Sakoparnig, Thomas and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Hondele, Maria and Jensen, Thomas E. and Hiller, Sebastian and Handschin, Christoph},
- doi = {10.1073/pnas.2105951118},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Proceedings of the National Academy of Sciences},
- number = {36},
- pages = {e2105951118},
- title = {{RNA}-bound {PGC}-1\${\textbackslash}upalpha\$ controls gene expression in liquid-like nuclear condensates},
- url = {https://doi.org/10.1073/pnas.2105951118},
- volume = {118},
- year = {2021}
-}
-
-@article{perezriverol_scalable_2019,
- abstract = {The recent improvements in mass spectrometry instruments and new analytical methods are increasing the intersection between proteomics and big data science. In addition, bioinformatics analysis is becoming increasingly complex and convoluted, involving multiple algorithms and tools. A wide variety of methods and software tools have been developed for computational proteomics and metabolomics during recent years, and this trend is likely to continue. However, most of the computational proteomics and metabolomics tools are designed as single-tiered software application where the analytics tasks can't be distributed, limiting the scalability and reproducibility of the data analysis. In this paper we summarise the key steps of metabolomics and proteomics data processing, including the main tools and software used to perform the data analysis. We discuss the combination of software containers with workflows environments for large scale metabolomics and proteomics analysis. Finally, we introduce to the proteomics and metabolomics communities a new approach for reproducible and large-scale data analysis based on BioContainers and two of the most popular workflow environments: Galaxy and Nextflow. This article is protected by copyright. All rights reserved},
- author = {Perez‐Riverol, Yasset and Moreno, Pablo},
- copyright = {This article is protected by copyright. All rights reserved},
- doi = {10.1002/pmic.201900147},
- issn = {1615-9861},
- journal = {PROTEOMICS},
- keywords = {+Galactic, +IsGalaxy, +RefPublic, +Reproducibility, +Tools, {\textgreater}Galaxy-P, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}Workflow4Metabolomics},
- language = {en},
- month = {October},
- number = {n/a},
- pages = {1900147},
- title = {Scalable {Data} {Analysis} in {Proteomics} and {Metabolomics} {Using} {BioContainers} and {Workflows} {Engines}},
- url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201900147},
- urldate = {2019-11-27},
- volume = {n/a},
- year = {2019}
-}
-
-@article{peters_metabolic_2021,
- author = {Peters, Kristian and Herman, Stephanie and Khoonsari, Payam Emami and Burman, Joachim and Neumann, Steffen and Kultima, Kim},
- doi = {10.1038/s41598-021-97491-1},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid},
- url = {https://doi.org/10.1038/s41598-021-97491-1},
- volume = {11},
- year = {2021}
-}
-
-@article{phan_transcriptome_2021,
- author = {Phan, Isabelle Q. and Rice, Christopher A. and Craig, Justin and Noorai, Rooksana E. and McDonald, Jacquelyn R. and Subramanian, Sandhya and Tillery, Logan and Barrett, Lynn K. and Shankar, Vijay and Morris, James C. and Voorhis, Wesley C. Van and Kyle, Dennis E. and Myler, Peter J.},
- doi = {10.1038/s41598-021-99903-8},
- journal = {Scientific Reports},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {November},
- note = {Publisher: Springer Science and Business Media LLC},
- number = {1},
- title = {The transcriptome of {Balamuthia} mandrillaris trophozoites for structure-guided drug design},
- url = {https://doi.org/10.1038/s41598-021-99903-8},
- volume = {11},
- year = {2021}
-}
-
-@article{pinter_functional_2021,
- abstract = {The lysine specific demethylase 1 (LSD1) plays a pivotal role in cellular differentiation by regulating the expression of key developmental genes in concert with different coregulatory proteins. This process is impaired in different cancer types and incompletely understood. To comprehensively identify functional coregulators of LSD1, we established a novel tractable fluorescent reporter system to monitor LSD1 activity in living cells. Combining this reporter system with a state-of-the-art multiplexed RNAi screen, we identify the DEAD-box helicase 19A (DDX19A) as a novel coregulator and demonstrate that suppression of Ddx19a results in an increase of R-loops and reduced LSD1-mediated gene silencing. We further show that DDX19A binds to tri-methylated lysine 27 of histone 3 (H3K27me3) and it regulates gene expression through the removal of transcription promoting R-loops. Our results uncover a novel transcriptional regulatory cascade where the downregulation of genes is dependent on the LSD1 mediated demethylation of histone H3 lysine 4 (H3K4). This allows the polycomb repressive complex 2 (PRC2) to methylate H3K27, which serves as a binding site for DDX19A. Finally, the binding of DDX19A leads to the efficient removal of R-loops at active promoters, which further de-represses LSD1 and PRC2, establishing a positive feedback loop leading to a robust repression of the target gene.},
- author = {Pinter, Sabine and Knodel, Franziska and Choudalakis, Michel and Schnee, Philipp and Kroll, Carolin and Fuchs, Marina and Broehm, Alexander and Weirich, Sara and Roth, Mareike and Eisler, Stephan A and Zuber, Johannes and Jeltsch, Albert and Rathert, Philipp},
- doi = {10.1093/nar/gkab180},
- issn = {0305-1048},
- journal = {Nucleic Acids Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {May},
- number = {8},
- pages = {4350--4370},
- title = {A functional {LSD1} coregulator screen reveals a novel transcriptional regulatory cascade connecting {R}-loop homeostasis with epigenetic regulation},
- url = {https://doi.org/10.1093/nar/gkab180},
- urldate = {2021-07-18},
- volume = {49},
- year = {2021}
-}
-
-@article{poulose_vprbp_2021,
- author = {Poulose, Ninu and Polonski, Adam and Forsythe, Nicholas and Gregg, Gemma and Maguire, Sarah and Fuchs, Marc and Minner, Sarah and McDade, Simon S. and Mills, Ian G.},
- doi = {10.1101/2021.02.28.433236},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {{VPRBP} functions downstream of the androgen receptor and {OGT} to restrict p53 activation in prostate cancer},
- url = {https://doi.org/10.1101/2021.02.28.433236},
- year = {2021}
-}
-
-@article{prislan_proof_2019,
- author = {Prislan, Iztok and Sajko, Sara and Poklar Ulrih, Nataša and Fürst, Luka},
- doi = {10.1039/C9RA09800C},
- journal = {RSC Advances},
- keywords = {+RefPublic, {\textgreater}RNA Workbench},
- language = {en},
- number = {71},
- pages = {41453--41461},
- title = {Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding},
- url = {https://pubs.rsc.org/en/content/articlelanding/2019/ra/c9ra09800c},
- urldate = {2020-01-05},
- volume = {9},
- year = {2019}
-}
-
-@article{qi_secreted_2020,
- abstract = {{\textless}p{\textgreater}Multicellular organisms coordinate tissue specific response to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, secreted small RNAs have recently been reported to regulate gene expression across tissue boundaries. Here we show that the conserved poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature in C. elegans. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 transmits environmental information across tissue boundaries and contributes to maintenance of stem cell immortality probably via retaining a stem cell specific program of gene expression.{\textless}/p{\textgreater}},
- author = {Qi, Wenjing and Gromoff, Erika D. v and Xu, Fan and Zhao, Qian and Yang, Wei and Pfeifer, Dietmar and Maier, Wolfgang and Long, Lijiang and Baumeister, Ralf},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/2020.12.04.408260},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {December},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.12.04.408260},
- title = {A secreted endoribonuclease {ENDU}-2 from the soma protects germline immortality in {C}. elegans},
- url = {https://www.biorxiv.org/content/10.1101/2020.12.04.408260v2},
- urldate = {2020-12-30},
- year = {2020}
-}
-
-@article{ragot_edna_2022,
- author = {Ragot, Rose and Villemur, Richard},
- journal = {Environmental monitoring and assessment},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Springer},
- number = {2},
- pages = {1--13},
- title = {{eDNA} profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters},
- volume = {194},
- year = {2022}
-}
-
-@article{rajczewski_rigorous_2021,
- abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.},
- author = {Rajczewski, Andrew T. and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James E. and McGowan, Thomas and Griffin, Timothy J. and Jagtap, Pratik D.},
- doi = {10.1186/s12014-021-09321-1},
- issn = {1559-0275},
- journal = {Clinical Proteomics},
- keywords = {+Galactic, +Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu, Bioinformatics, Mass spectrometry, Pandemic, Peptide-detection, Viral proteome, Workflows},
- month = {May},
- number = {1},
- pages = {15},
- title = {A rigorous evaluation of optimal peptide targets for {MS}-based clinical diagnostics of {Coronavirus} {Disease} 2019 ({COVID}-19)},
- url = {https://doi.org/10.1186/s12014-021-09321-1},
- urldate = {2021-05-11},
- volume = {18},
- year = {2021}
-}
-
-@article{ranchou-peyruse_microbial_2021,
- author = {Ranchou-Peyruse, Magali and Guignard, Marion and Casteran, Franck and Abadie, Maïder and Defois, Clémence and Peyret, Pierre and Dequidt, David and Caumette, Guilhem and Chiquet, Pierre and Cézac, Pierre and Ranchou-Peyruse, Anthony},
- doi = {10.3389/fmicb.2021.688929},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {October},
- note = {Publisher: Frontiers Media SA},
- title = {Microbial {Diversity} {Under} the {Influence} of {Natural} {Gas} {Storage} in a {Deep} {Aquifer}},
- url = {https://doi.org/10.3389/fmicb.2021.688929},
- volume = {12},
- year = {2021}
-}
-
-@article{rasche_galactic_2020,
- abstract = {AbstractBackground.  Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the f},
- author = {Rasche, Helena and Hiltemann, Saskia},
- doi = {10.1093/gigascience/giaa065},
- journal = {GigaScience},
- keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {June},
- note = {Publisher: Oxford Academic},
- number = {6},
- shorttitle = {Galactic {Circos}},
- title = {Galactic {Circos}: {User}-friendly {Circos} plots within the {Galaxy} platform},
- url = {https://academic.oup.com/gigascience/article/9/6/giaa065/5856406},
- urldate = {2020-08-18},
- volume = {9},
- year = {2020}
-}
-
-@article{rasche_training_2020,
- abstract = {{\textless}p{\textgreater}Background: Hands-on training, whether it is in Bioinformatics or other scientific domains, requires significant resources and knowledge to setup and run. Trainers must have access to infrastructure that can support the sudden spike in usage, with classes of 30 or more trainees simultaneously running resource-intensive tools. For efficient classes, the jobs must run quickly, without queuing delays, lest they disrupt the timetable set out for the class. Often times this is achieved via running on a private server where there is no contention for the queue, and therefore no or minimal waiting time. However, this requires the teacher or trainer to have the technical knowledge to manage compute infrastructure, in addition to their didactic responsibilities. This presents significant burdens to potential training events, in terms of infrastructure cost, person-hours of preparation, technical knowledge, and available staff to manage such events. Findings: Galaxy Europe has developed Training Infrastructure as a Service (TIaaS) which we provide to the scientific commnuity as a service built on top of the Galaxy Platform. Training event organisers request a training and Galaxy administrators can allocate private queues specifically for the training. Trainees are transparently placed in a private queue where their jobs run without delay. Trainers access the dashboard of the TIaaS Service and can remotely follow the progress of their trainees without in-person interactions. Conclusions: TIaaS on Galaxy Europe provides reusable and fast infrastructure for Galaxy training. The instructor dashboard provides visibility into class progress, making in-person trainings more efficient and remote training possible. In the past 24 months, \$\>110\$ trainings with over 3000 trainees have used this infrastructure for training, across scientific domains, all enjoying the accessibility and reproducibility of Galaxy for training the next generation of bioinformaticians. TIaaS itself is an extension to Galaxy which can be deployed by any Galaxy administrator to provide similar benefits for their users. https://galaxyproject.eu/tiaas{\textless}/p{\textgreater}},
- author = {Rasche, Helena and Gruening, Bjoern Andreas},
- copyright = {© 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
- doi = {10.1101/2020.08.23.263509},
- journal = {bioRxiv},
- keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2020.08.23.263509},
- title = {Training {Infrastructure} as a {Service}},
- url = {https://www.biorxiv.org/content/10.1101/2020.08.23.263509v1},
- urldate = {2020-08-25},
- year = {2020}
-}
-
-@article{rasche_usegalaxyeu_2019,
- abstract = {Read this work by Rasche H, at F1000Research.},
- author = {Rasche, Helena and Europe, Galaxy Project},
- doi = {10.7490/f1000research.1117097.1},
- journal = {F1000Research},
- keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}UseGalaxy.eu},
- month = {July},
- shorttitle = {{\textless}p{\textgreater}{UseGalaxy}.eu},
- title = {{UseGalaxy}.eu: {Community}, {Training}, {Infrastructure}, and {Users}},
- url = {https://f1000research.com/posters/8-1154},
- urldate = {2020-08-21},
- volume = {8},
- year = {2019}
-}
-
-@article{rauschmeier_bhlhe40_2019,
- abstract = {Abstract Tissues in multicellular organisms are populated by resident macrophages, which perform both generic and tissue-specific functions. The latter are induced by signals from the microenvironment and rely on unique tissue-specific molecular programs requiring the combinatorial action of tissue-specific and broadly expressed transcriptional regulators. Here, we identify the transcription factors Bhlhe40 and Bhlhe41 as novel regulators of alveolar macrophages (AMs)?a population that provides the first line of immune defense and executes homeostatic functions in lung alveoli. In the absence of these factors, AMs exhibited decreased proliferation that resulted in a severe disadvantage of knockout AMs in a competitive setting. Gene expression analyses revealed a broad cell-intrinsic footprint of Bhlhe40/Bhlhe41 deficiency manifested by a downregulation of AM signature genes and induction of signature genes of other macrophage lineages. Genome-wide characterization of Bhlhe40 DNA binding suggested that these transcription factors directly repress the expression of lineage-inappropriate genes in AMs. Taken together, these results identify Bhlhe40 and Bhlhe41 as key regulators of AM self-renewal and guardians of their identity.},
- author = {Rauschmeier, René and Gustafsson, Charlotte and Reinhardt, Annika and A-Gonzalez, Noelia and Tortola, Luigi and Cansever, Dilay and Subramanian, Sethuraman and Taneja, Reshma and Rossner, Moritz J and Sieweke, Michael H and Greter, Melanie and Månsson, Robert and Busslinger, Meinrad and Kreslavsky, Taras},
- doi = {10.15252/embj.2018101233},
- issn = {0261-4189},
- journal = {The EMBO Journal},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Bhlhe40, Bhlhe41, alveolar macrophages, self-renewal, tissue-resident macrophages},
- month = {August},
- number = {0},
- pages = {e101233},
- title = {Bhlhe40 and {Bhlhe41} transcription factors regulate alveolar macrophage self-renewal and identity},
- url = {https://www.embopress.org/doi/abs/10.15252/embj.2018101233},
- urldate = {2019-09-19},
- volume = {0},
- year = {2019}
-}
-
-@article{rauschmeier_cell-intrinsic_2021,
- abstract = {{\textless}h3{\textgreater}ABSTRACT{\textless}/h3{\textgreater} {\textless}p{\textgreater}The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction – a process that relies on a complex interplay between specialized effector subsets of B and CD4 T lymphocytes – GC B cells and T follicular helper (T$_{\textrm{FH}}$) cells. Intriguingly, several key positive regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation thus limiting the number of T$_{\textrm{FH}}$ cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Conditional Bhlhe40 inactivation confirmed cell-autonomous functions of Bhlhe40 in both GC B and T$_{\textrm{FH}}$ cells, while the GC phenotype was further enhanced upon loss of Bhlhe40 in both cell types. This negative regulation of the GC reaction by Bhlhe40 was of crucial importance, as Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by accumulation of monoclonal GC B-like cells and polyclonal T$_{\textrm{FH}}$ cells in various tissues.{\textless}/p{\textgreater}},
- author = {Rauschmeier, René and Reinhardt, Annika and Gustafsson, Charlotte and Glaros, Vassilis and Artemov, Artem V. and Taneja, Reshma and Adameyko, Igor and Månsson, Robert and Busslinger, Meinrad and Kreslavsky, Taras},
- copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
- doi = {10.1101/2021.03.12.435122},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2021.03.12.435122},
- title = {Cell-intrinsic functions of the transcription factor {Bhlhe40} in activated {B} cells and {T} follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis},
- url = {https://www.biorxiv.org/content/10.1101/2021.03.12.435122v1},
- urldate = {2021-07-21},
- year = {2021}
-}
-
-@article{retamal-morales_draft_2018,
- abstract = {Biosurfactants are amphipathic molecules with relevance in biotechnology due to their structural diversity, low toxicity and biodegradability. The genus Rhodococcus has extensively been studied because of its capacity to produce trehalose-containing surfactants as well as trehalose lipids as potential pathogenic factor. Here we present the draft genome sequence of Rhodococcus erythropolis B7g isolated with toluene from fuel-contaminated soil. The genome comprises 7,175,690 bp in 121 contigs, a G + C content of 62,4\% and 7,153 coding DNA sequences (CDSs), and it contains genes for trehalose biosynthesis and surfactant production. Additionally, genes for the production of trehalose-tetraester biosurfactant were identified, whose function was experimentally verified making the strain B7g a potential candidate for use in bioremediation applications or in biosurfactant exploration.},
- author = {Retamal-Morales, Gerardo and Heine, Thomas and Tischler, Judith S. and Erler, Beate and Gröning, Janosch A. D. and Kaschabek, Stefan R. and Schlömann, Michael and Levicán, Gloria and Tischler, Dirk},
- doi = {10.1016/j.jbiotec.2018.06.001},
- issn = {0168-1656},
- journal = {Journal of Biotechnology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Actinobacteria, Biosurfactants, Genome mining, Gram-positive, Mycolic acids, Trehalose},
- month = {August},
- pages = {38--41},
- title = {Draft genome sequence of {Rhodococcus} erythropolis {B7g}, a biosurfactant producing actinobacterium},
- url = {http://www.sciencedirect.com/science/article/pii/S0168165618301767},
- urldate = {2018-07-17},
- volume = {280},
- year = {2018}
-}
-
-@article{riediger_analysis_2020,
- author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.},
- doi = {10.1093/plcell/koaa017},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {December},
- note = {Publisher: Oxford University Press (OUP)},
- number = {2},
- pages = {248--269},
- title = {Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing ({Grad}-seq)},
- url = {https://doi.org/10.1093/plcell/koaa017},
- volume = {33},
- year = {2020}
-}
-
-@article{rogg_srgap1_2021,
- author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph},
- doi = {10.1681/asn.2020081126},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {January},
- note = {Publisher: American Society of Nephrology (ASN)},
- number = {3},
- pages = {563--579},
- title = {{SRGAP1} {Controls} {Small} {Rho} {GTPases} {To} {Regulate} {Podocyte} {Foot} {Process} {Maintenance}},
- url = {https://doi.org/10.1681/asn.2020081126},
- volume = {32},
- year = {2021}
-}
-
-@article{roland_wirth_microbiomes_2020,
- abstract = {Background: Comparison of the microbiomes in supragingival biofilm and saliva samples collected from juvenile patients developing induced or spontaneous gingivitis with healthy controls.Results: 36 supragingival biofilm samples from 9 a...},
- author = {{Roland Wirth}},
- doi = {10.21203/rs.3.rs-45630/v1},
- journal = {Research Square},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- title = {Microbiomes in {Supragingival} {Biofilms} and {Saliva} of {Adolescent} {Patients} with {Induced} and {Naturally} {Occurring} {Gingivitis} {Relative} to {Gingival} {Health}},
- url = {https://www.researchsquare.com/article/rs-45630/v1},
- urldate = {2020-08-19},
- year = {2020}
-}
-
-@article{roncoroni_sars-cov-2_2021,
- author = {Roncoroni, Miguel and Droesbeke, Bert and Eguinoa, Ignacio and Ruyck, Kim De and D'Anna, Flora and Yusuf, Dilmurat and Grüning, Björn and Backofen, Rolf and Coppens, Frederik},
- doi = {10.1093/bioinformatics/btab421},
- editor = {Lu, Zhiyong},
- journal = {Bioinformatics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: Oxford University Press (OUP)},
- title = {A {SARS}-{CoV}-2 sequence submission tool for the {European} {Nucleotide} {Archive}},
- url = {https://doi.org/10.1093/bioinformatics/btab421},
- year = {2021}
-}
-
-@article{roquis_genomic_2021,
- author = {Roquis, David and Robertson, Marta and Yu, Liang and Thieme, Michael and Julkowska, Magdalena and Bucher, Etienne},
- doi = {10.1093/nar/gkab828},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- note = {Publisher: Oxford University Press (OUP)},
- number = {18},
- pages = {10431--10447},
- title = {Genomic impact of stress-induced transposable element mobility in {Arabidopsis}},
- url = {https://doi.org/10.1093/nar/gkab828},
- volume = {49},
- year = {2021}
-}
-
-@phdthesis{sabrina_statistical_2020,
- abstract = {Protein-RNA interactions play an important role in all post-transcriptional regulatory processes. High throughput detection of protein-RNA interactions has been facilitated by the emerging CLIP-seq (crosslinking and immunoprecipitation combined with high-throughput sequencing) techniques. Enrichments in mapped reads as well as base transitions or deletions at crosslink sites can be used to infer binding regions. Single-nucleotide resolution techniques (iCLIP and eCLIP) have been achieved by capturing high fractions of cDNAs which are truncated at protein-RNA crosslink sites. Increasing numbers of datasets and derivatives of these protocols have been published in recent years, requiring tailored computational analyses. Existing methods unfortunately do not explicitly model the specifics of truncation patterns and possible biases caused by background binding or crosslinking sequence preferences. 
-We present PureCLIP, a hidden Markov model based approach, which simultaneously performs peak calling and individual crosslink site detection. It is capable of incorporating external data to correct for non-specific background signals and, for the first time, for the crosslinking biases. We devised a comprehensive evaluation based on three strategies. Firstly, we developed a workflow to simulate iCLIP data, which starts from real RNA-seq data and known binding regions and then mimics the experimental steps of the iCLIP protocol, including the generation of background signals. Secondly, we used experimental iCLIP and eCLIP datasets, using the proteins’ known predominant binding regions. And thirdly, we assessed the agreement of called sites between replicates, assuming target-specific signals are reproducible between replicates. 
-On both simulated and real data, PureCLIP is consistently more precise in calling crosslink sites than other state-of-the-art methods. In particular when incorporating input control data and crosslink associated motifs (CL-motifs) PureCLIP is up to 13\% more precise than other methods and we show that it has an up to 20\% higher agreement across replicates. Moreover, our method can optionally merge called crosslink sites to binding regions based on their distance and we show that the resulting regions reflect the known binding regions with high-resolution. 
-Additionally, we demonstrate that our method achieves a high precision robustly over a range of different settings and performs well for proteins with different binding characteristics. Lastly, we extended the method to include individual CLIP replicates and show that this can boost the precision even further. PureCLIP and its documenta- tion are publicly available at https://github.com/skrakau/PureCLIP.},
- author = {Sabrina, Krakau},
- copyright = {https://creativecommons.org/licenses/by-sa/4.0/},
- keywords = {+Tools, {\textgreater}UseGalaxy.eu},
- language = {eng},
- school = {Freien Universität Berlin},
- title = {Statistical models to capture protein-{RNA} interaction footprints from truncation-based {CLIP}-seq data},
- url = {https://refubium.fu-berlin.de/handle/fub188/26406},
- urldate = {2020-01-29},
- year = {2020}
-}
-
-@article{sajulga_survey_2020,
- abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.},
- author = {Sajulga, Ray and Easterly, Caleb and Riffle, Michael and Mesuere, Bart and Muth, Thilo and Mehta, Subina and Kumar, Praveen and Johnson, James and Gruening, Bjoern Andreas and Schiebenhoefer, Henning and Kolmeder, Carolin A. and Fuchs, Stephan and Nunn, Brook L. and Rudney, Joel and Griffin, Timothy J. and Jagtap, Pratik D.},
- doi = {10.1371/journal.pone.0241503},
- issn = {1932-6203},
- journal = {PLOS ONE},
- keywords = {+Methods, +RefPublic, +Stellar, +Tools, +UseLocal, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu, BLAST algorithm, Computer software, Database searching, Functional analysis, Gene ontologies, Microbiome, Software tools, Taxonomy},
- language = {en},
- month = {November},
- note = {Publisher: Public Library of Science},
- number = {11},
- pages = {e0241503},
- title = {Survey of metaproteomics software tools for functional microbiome analysis},
- url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241503},
- urldate = {2020-11-11},
- volume = {15},
- year = {2020}
-}
-
-@incollection{saleh_nascent_2021,
- author = {Saleh, Omar and Dwiani, Sarlita and Rott, Julia and Kühn, Kristina},
- booktitle = {Methods in {Molecular} {Biology}},
- doi = {10.1007/978-1-0716-1653-6_19},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {September},
- pages = {279--300},
- publisher = {Springer US},
- title = {Nascent {Transcript} {Sequencing} for the {Mapping} of {Promoters} in thaliana {Mitochondria}},
- url = {https://doi.org/10.1007/978-1-0716-1653-6_19},
- year = {2021}
-}
-
-@article{sanchez_pathwaymatcher_2019,
- abstract = {AbstractBackground.  Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., g},
- author = {Sánchez, Luis Francisco Hernández and Burger, Bram and Horro, Carlos and Fabregat, Antonio and Johansson, Stefan and Njølstad, Pål Rasmus and Barsnes, Harald and Hermjakob, Henning and Vaudel, Marc},
- doi = {10.1093/gigascience/giz088},
- journal = {GigaScience},
- keywords = {+Tools, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {August},
- note = {Publisher: Oxford Academic},
- number = {8},
- shorttitle = {{PathwayMatcher}},
- title = {{PathwayMatcher}: proteoform-centric network construction enables fine-granularity multiomics pathway mapping},
- url = {https://academic.oup.com/gigascience/article/8/8/giz088/5541632},
- urldate = {2020-08-16},
- volume = {8},
- year = {2019}
-}
-
-@article{sauriol_modeling_2020,
- abstract = {Cancer cell lines are amongst the most important pre-clinical models. In the context of epithelial ovarian cancer, a highly heterogeneous disease with diverse subtypes, it is paramount to study a wide panel of models in order to draw a representative picture of the disease. As this lethal gynaecological malignancy has seen little improvement in overall survival in the last decade, it is all the more pressing to support future research with robust and diverse study models. Here, we describe ten novel spontaneously immortalized patient-derived ovarian cancer cell lines, detailing their respective mutational profiles and gene/biomarker expression patterns, as well as their in vitro and in vivo growth characteristics. Eight of the cell lines were classified as high-grade serous, while two were determined to be of the rarer mucinous and clear cell subtypes, respectively. Each of the ten cell lines presents a panel of characteristics reflective of diverse clinically relevant phenomena, including chemotherapeutic resistance, metastatic potential, and subtype-associated mutations and gene/protein expression profiles. Importantly, four cell lines formed subcutaneous tumors in mice, a key characteristic for pre-clinical drug testing. Our work thus contributes significantly to the available models for the study of ovarian cancer, supplying additional tools to better understand this complex disease.},
- author = {Sauriol, Alexandre and Simeone, Kayla and Portelance, Lise and Meunier, Liliane and Leclerc-Desaulniers, Kim and de Ladurantaye, Manon and Chergui, Meriem and Kendall-Dupont, Jennifer and Rahimi, Kurosh and Carmona, Euridice and Provencher, Diane M. and Mes-Masson, Anne-Marie},
- copyright = {http://creativecommons.org/licenses/by/3.0/},
- doi = {10.3390/cancers12082222},
- journal = {Cancers},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, biomarkers, carboplatin, cell lines, clear cell, epithelial ovarian cancer, gene expression, high-grade serous, mucinous, mutation profile, xenograft},
- language = {en},
- month = {August},
- note = {Number: 8
-Publisher: Multidisciplinary Digital Publishing Institute},
- number = {8},
- pages = {2222},
- title = {Modeling the {Diversity} of {Epithelial} {Ovarian} {Cancer} through {Ten} {Novel} {Well} {Characterized} {Cell} {Lines} {Covering} {Multiple} {Subtypes} of the {Disease}},
- url = {https://www.mdpi.com/2072-6694/12/8/2222},
- urldate = {2021-04-09},
- volume = {12},
- year = {2020}
-}
-
-@article{schafer_glassgo_2020,
- abstract = {AbstractMotivation.  The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is f},
- author = {Schäfer, Richard A. and Lott, Steffen C. and Georg, Jens and Grüning, Björn A. and Hess, Wolfgang R. and Voß, Björn},
- doi = {10.1093/bioinformatics/btaa556},
- journal = {Bioinformatics},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}RNA Workbench},
- language = {en},
- month = {June},
- shorttitle = {{GLASSGo} in {Galaxy}},
- title = {{GLASSGo} in {Galaxy}: high-throughput, reproducible and easy-to-integrate prediction of {sRNA} homologs},
- url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa556/5850859},
- urldate = {2020-06-09},
- year = {2020}
-}
-
-@article{schlecht_transcriptomic_2020,
- abstract = {Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) in body donor eyes with neovascular age-related macular degeneration (nAMD) and were thus limited by the time span from death to preservation and the associated 5'-RNA degradation. Therefore, this study used CNV and control specimens which had been formalin-fixed and paraffin-embedded immediately after surgical extraction and analyzed them using a 3’ RNA sequencing approach. Transcriptome profiles were analyzed and used to estimate content of immune and stromal cells and to define disease-associated gene signatures using statistical and bioinformatic methods. We identified 158 differentially-expressed genes (DEG) that were significantly increased in CNV compared to control tissue. Cell type enrichment analysis revealed a diverse cellular landscape with an enrichment of immune and stroma cell types in CNV including endothelial cells, macrophages, T cells and NKT cells. Gene ontology enrichment analysis demonstrated that DEG contributed to Blood Vessel Development, Extracellular Structure Organization, Response to Wounding and several immune-related terms. The S100 calcium-binding protein A8 (S100A8) and S100A9 emerged among the top DEG, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples. This study provides a high-resolution RNA-sequencing-based transcriptional signature of human CNV, characterizes its compositional pattern of immune and stromal cells and reveals S100A8/A9 as a novel biomarker and promising target for AMD-directed therapeutics and diagnostics.},
- author = {Schlecht, Anja and Boneva, Stefaniya and Gruber, Markus and Zhang, Peipei and Horres, Ralf and Bucher, Felicitas and Auw-Haedrich, Claudia and Hansen, Lutz and Stahl, Andreas and Hilgendorf, Ingo and Agostini, Hansjürgen and Wieghofer, Peter and Schlunck, Günther and Wolf, Julian and Lange, Clemens AK.},
- doi = {10.1016/j.ajpath.2020.04.004},
- issn = {0002-9440},
- journal = {The American Journal of Pathology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {April},
- title = {Transcriptomic {Characterization} of {Human} {Choroidal} {Neovascular} {Membranes} {Identifies} {Calprotectin} as a {Novel} {Biomarker} for {Patients} with {Age}-related {Macular} {Degeneration}},
- url = {http://www.sciencedirect.com/science/article/pii/S0002944020302017},
- urldate = {2020-05-28},
- year = {2020}
-}
-
-@article{senapathi_biomolecular_2019,
- abstract = {Motivation.  The pathway from genomics through proteomics and onto a molecular description of biochemical processes make the discovery of drugs and biom},
- author = {Senapathi, Tharindu and Bray, Simon and Barnett, Christopher B. and Grüning, Björn and Naidoo, Kevin J.},
- doi = {10.1093/bioinformatics/btz107},
- journal = {Bioinformatics},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}BRIDGE, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {February},
- title = {Biomolecular {Reaction} \& {Interaction} {Dynamics} {Global} {Environment} ({BRIDGE})},
- url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz107/5317160},
- urldate = {2019-02-21},
- year = {2019}
-}
-
-@article{senapathi_bridge_2020,
- abstract = {Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a challenge. Here we show how Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE), an open-source web-based compute and analytics platform for computational chemistry developed based on the Galaxy bioinformatics platform, makes protocol sharing seamless following genomics and proteomics. BRIDGE makes available tools and workflows to carry out protein molecular dynamics simulations and accurate free energy computations of protein-ligand binding. We illustrate the dynamics and simulation protocols for predicting protein-ligand binding affinities in silico on the T4 lysozyme system. This protocol is suitable for both novice and experienced practitioners. We show that with BRIDGE, protocols can be shared with collaborators or made publicly available, thus making simulation results and computations independently verifiable and reproducible., Bio-protocol is an online peer-reviewed protocol journal. Its mission is to make life science research more efficient and reproducible by curating and hosting high quality, free access protocols.},
- author = {Senapathi, Tharindu and Barnett, Christopher B. and Naidoo, Kevin J.},
- doi = {10.21769/BioProtoc.3731},
- journal = {Bio-protocol},
- keywords = {+Galactic, +HowTo, +IsGalaxy, +Shared, {\textgreater}BRIDGE, {\textgreater}ChemicalToolbox},
- month = {September},
- number = {17},
- pages = {e3731--e3731},
- shorttitle = {{BRIDGE}},
- title = {{BRIDGE}: {An} {Open} {Platform} for {Reproducible} {Protein}-{Ligand} {Simulations} and {Free} {Energy} of {Binding} {Calculations}},
- url = {https://bio-protocol.org/e3731},
- urldate = {2020-09-09},
- volume = {10},
- year = {2020}
-}
-
-@article{sharma_pan-cancer_2019,
- abstract = {Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, RNA folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous mutations found in human cancer and characterize their properties. We provide the user-friendly, comprehensive resource for synonymous mutations in cancer, SynMICdb (http://SynMICdb.dkfz.de), which also contains orthogonal information about gene annotation, recurrence, mutation loads, cancer association, conservation, alternative events, impact on mRNA structure and a SynMICdb score. Notably, synonymous and missense mutations are depleted at the 5'-end of the coding sequence as well as at the ends of internal exons independent of mutational signatures. For patient-derived synonymous mutations in the oncogene KRAS, we indicate that single point mutations can have a relevant impact on expression as well as on mRNA secondary structure., Synonymous mutations do not alter amino acid sequence but may exert oncogenic effects in other ways. Here, the authors present a catalogue of synonymous mutations in cancer and characterise their properties.},
- author = {Sharma, Yogita and Miladi, Milad and Dukare, Sandeep and Boulay, Karine and Caudron-Herger, Maiwen and Groß, Matthias and Backofen, Rolf and Diederichs, Sven},
- doi = {10.1038/s41467-019-10489-2},
- issn = {2041-1723},
- journal = {Nature Communications},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- pmcid = {PMC6562042},
- pmid = {31189880},
- title = {A pan-cancer analysis of synonymous mutations},
- url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562042/},
- urldate = {2019-07-25},
- volume = {10},
- year = {2019}
-}
-
-@article{shi_recapitulating_2022,
- author = {Shi, Shaojun and Verstegen, Monique MA and Roest, Henk P and Ardisasmita, Arif I and Cao, Wanlu and Roos, Floris JM and de Ruiter, Petra E and Niemeijer, Marije and Pan, Qiuwei and IJzermans, Jan NM and {others}},
- journal = {Cellular and Molecular Gastroenterology and Hepatology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Elsevier},
- number = {2},
- pages = {541--564},
- title = {Recapitulating {Cholangiopathy}-{Associated} {Necroptotic} {Cell} {Death} {In} {Vitro} {Using} {Human} {Cholangiocyte} {Organoids}},
- volume = {13},
- year = {2022}
-}
-
-@article{shi_recapitulating_2022-1,
- author = {Shi, Shaojun and Verstegen, Monique M. A. and Roest, Henk P. and Ardisasmita, Arif I. and Cao, Wanlu and Roos, Floris J. M. and Ruiter, Petra E. de and Niemeijer, Marije and Pan, Qiuwei and IJzermans, Jan N. M. and Laan, Luc J. W. van der},
- doi = {10.1016/j.jcmgh.2021.10.009},
- journal = {Cellular and Molecular Gastroenterology and Hepatology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Elsevier BV},
- number = {2},
- pages = {541--564},
- title = {Recapitulating {Cholangiopathy}-{Associated} {Necroptotic} {Cell} {Death} {In} {Vitro} {Using} {Human} {Cholangiocyte} {Organoids}},
- url = {https://doi.org/10.1016/j.jcmgh.2021.10.009},
- volume = {13},
- year = {2022}
-}
-
-@article{simon-chica_novel_2021,
- abstract = {Macrophages (MΦ), known for immunological roles such as phagocytosis and antigen presentation, have been found to electrotonically couple to cardiomyocytes (CM) of the atrio-ventricular node via Cx43, affecting cardiac conduction in isolated mouse hearts. Here, we characterise passive and active electrophysiological properties of murine cardiac resident MΦ, and model their potential electrophysiological relevance for CM.We combined classic electrophysiological approaches with 3 D florescence imaging, RNA-sequencing, pharmacological interventions and computer simulations. We used Cx3cr1eYFP/+ mice wherein cardiac MΦ were fluorescently labelled. FACS-purified fluorescent MΦ from mouse hearts were studied by whole-cell patch-clamp. MΦ electrophysiological properties include: membrane resistance 2.2 ± 0.1 GΩ (all data mean±SEM), capacitance 18.3 ± 0.1 pF, resting membrane potential -39.6 ± 0.3 mV, and several voltage-activated, outward or inwardly-rectifying potassium currents. Using ion channel blockers (barium, TEA, 4-AP, margatoxin, XEN-D0103, DIDS), flow cytometry, immuno-staining and RNA-sequencing, we identified Kv1.3, Kv1.5 and Kir2.1 as channels contributing to observed ion currents. MΦ displayed four patterns for outward and two for inward-rectifier potassium currents. Additionally, MΦ showed surface expression of Cx43, a prerequisite for homo- and/or heterotypic electrotonic coupling. Experimental results fed into development of an original computational model to describe cardiac MΦ electrophysiology. Computer simulations to quantitatively assess plausible effects of MΦ on electrotonically coupled CM showed that MΦ can depolarise resting CM, shorten early and prolong late action potential duration, with effects depending on coupling strength and individual MΦ electrophysiological properties, in particular resting membrane potential and presence/absence of Kir2.1.Our results provide a first electrophysiological characterisation of cardiac resident MΦ, and a computational model to quantitatively explore their relevance in the heterocellular heart. Future work will be focussed at distinguishing electrophysiological effects of MΦ–CM coupling on both cell types during steady-state and in patho-physiological remodelling, when immune cells change their phenotype, proliferate, and/or invade from external sources.Cardiac tissue contains resident macrophages (MΦ) which, beyond immunological and housekeeping roles, have been found to electrotonically couple via connexins to cardiomyocytes (CM), stabilising atrio-ventricular conduction at high excitation rates. Here, we characterise structure and electrophysiological function of murine cardiac MΦ and provide a computational model to quantitatively probe the potential relevance of MΦ-CM coupling for cardiac electrophysiology. We find that MΦ are unlikely to have major electrophysiological effects in normal tissue, where they would hasten early and slow late CM-repolarisation. Further work will address potential arrhythmogenicity of MΦ in patho-physiologically remodelled tissue containing elevated MΦ-numbers, incl. non-resident recruited cells.},
- author = {Simon-Chica, Ana and Fernández, Marbely C and Wülfers, Eike M and Lother, Achim and Hilgendorf, Ingo and Seemann, Gunnar and Ravens, Ursula and Kohl, Peter and Schneider-Warme, Franziska},
- doi = {10.1093/cvr/cvab126},
- issn = {0008-6363},
- journal = {Cardiovascular Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- number = {cvab126},
- shorttitle = {Novel insights into the electrophysiology of murine cardiac macrophages},
- title = {Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels},
- url = {https://doi.org/10.1093/cvr/cvab126},
- urldate = {2021-05-17},
- year = {2021}
-}
-
-@article{soares_hierarchical_2021,
- author = {Soares, Mário A. F. and Soares, Diogo S. and Teixeira, Vera and Heskol, Abeer and Bressan, Raul Bardini and Pollard, Steven M. and Oliveira, Raquel A. and Castro, Diogo S.},
- doi = {10.1101/gad.348174.120},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: Cold Spring Harbor Laboratory},
- number = {13-14},
- pages = {1020--1034},
- title = {Hierarchical reactivation of transcription during mitosis-to-{G1} transition by {Brn2} and {Ascl1} in neural stem cells},
- url = {https://doi.org/10.1101/gad.348174.120},
- volume = {35},
- year = {2021}
-}
-
-@article{spradling_mitochondrial_2021,
- author = {Spradling, Theresa A. and Place, Alexandra C. and Campbell, Ashley L. and Demastes, James W.},
- doi = {10.1371/journal.pone.0254138},
- editor = {Waller, Ross Frederick},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Public Library of Science (PLoS)},
- number = {7},
- pages = {e0254138},
- title = {Mitochondrial genome of {Geomydoecus} aurei, a pocket-gopher louse},
- url = {https://doi.org/10.1371/journal.pone.0254138},
- volume = {16},
- year = {2021}
-}
-
-@article{stachurova_beta-lactam_2021,
- abstract = {This work monitored the effect of a municipal and a village wastewater treatment plant (WWTP) technology on the fate of beta-lactam resistance genes in bacterial populations in different phases of the wastewater treatment process. In case of the municipal WWTP1, the bacteria possessing a high ampicillin resistance (minimal inhibitory concentration (MIC) values of 20 mg/mL) accumulated in the sedimentation tank, which was accompanied with a higher concentration of ampicillin in the wastewater samples (28.09 ng/L) and an increase in the relative abundance of the blaTEM gene in the bacterial population. However, an opposite trend was revealed with the blaNDM-1 gene, making the sedimentation processes of WWTP1 crucial only for the accumulation of the blaTEM gene. Similarly, the comparison with the WWTP2 showed that the accumulation of the ampicillin resistance in bacterial population probably depended on the WWTP technology and wastewater composition. Out of the four tested resistance genes (blaTEM, blaKPC, blaNDM-1, and blaOXA-48), blaTEM and blaNDM-1 genes were the only two detected in this study. According to NGS analysis of bacterial 16 S rRNA gene, Gammaproteobacteria dominated the ampicillin-resistant bacteria of the WWTP sedimentation tanks. Their relative abundance in the bacterial population also increased during the sedimentation processes in WWTP1. It could indicate the role of the bacterial taxon in ampicillin resistance accumulation in this WWTP and show that only 9.29\% of the original bacterial population from the nitrification tank is involved in the documented shifts in beta-lactam resistance of the bacterial population.},
- author = {Stachurová, Tereza and Piková, Hana and Bartas, Martin and Semerád, Jaroslav and Svobodová, Kateřina and Malachová, Kateřina},
- doi = {10.1016/j.chemosphere.2021.130749},
- issn = {0045-6535},
- journal = {Chemosphere},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Antibiotic resistance, Beta-lactam resistance genes, Wastewater treatment plant, blaNDM-1, blaTEM},
- language = {en},
- month = {October},
- pages = {130749},
- title = {Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants},
- url = {https://www.sciencedirect.com/science/article/pii/S0045653521012200},
- urldate = {2021-07-20},
- volume = {280},
- year = {2021}
-}
-
-@article{stein_single-cell_2021,
- author = {Stein, Catarina M. and Weiskirchen, Ralf and Damm, Frederik and Strzelecka, Paulina M.},
- doi = {10.1002/jcb.30134},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: Wiley},
- title = {Single-cell omics: {Overview}, analysis, and application in biomedical science},
- url = {https://doi.org/10.1002/jcb.30134},
- year = {2021}
-}
-
-@article{stephen_jr_comparative_2022,
- author = {Stephen Jr, DB and Jayaraman, Jayaraj and Ramsubhag, Adesh and {others}},
- journal = {PeerJ},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: PeerJ Inc.},
- pages = {e12632},
- title = {Comparative genomics of the black rot pathogen {Xanthomonas} campestris pv. campestris and non-pathogenic co-inhabitant {Xanthomonas} melonis from {Trinidad} reveal unique pathogenicity determinants and secretion system profiles},
- volume = {9},
- year = {2022}
-}
-
-@article{sun_complete_2021,
- author = {Sun, Shu-Wei and Huang, Jing-Chao and Liu, Yan-Qun},
- doi = {10.1080/23802359.2021.1945975},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Informa UK Limited},
- number = {8},
- pages = {2209--2211},
- title = {The complete mitochondrial genome of the wild silkmoth {Antheraea} yamamai from {Heilongjiang}, {China} ({Lepidoptera}: {Saturniidae})},
- url = {https://doi.org/10.1080/23802359.2021.1945975},
- volume = {6},
- year = {2021}
-}
-
-@article{sun_stencil_2022,
- author = {Sun, Qi and Nematbakhsh, Ali and Kuntala, Prashant K. and Kellogg, Gretta and Pugh, B. Franklin and Lai, William K. M.},
- doi = {10.1371/journal.pcbi.1009859},
- editor = {Pertea, Mihaela},
- journal = {PLOS Computational Biology},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Public Library of Science (PLoS)},
- number = {2},
- pages = {e1009859},
- title = {{STENCIL}: {A} web templating engine for visualizing and sharing life science datasets},
- url = {https://doi.org/10.1371/journal.pcbi.1009859},
- volume = {18},
- year = {2022}
-}
-
-@article{szachniuk_rnapolis:_2019,
- author = {Szachniuk, Marta},
- doi = {10.2478/fcds-2019-0012},
- journal = {Foundations of Computing and Decision Sciences},
- keywords = {+RefPublic, {\textgreater}RNA Workbench},
- language = {en},
- month = {June},
- number = {2},
- pages = {241--257},
- shorttitle = {{RNApolis}},
- title = {{RNApolis}: {Computational} {Platform} for {RNA} {Structure} {Analysis}},
- url = {https://content.sciendo.com/view/journals/fcds/44/2/article-p241.xml},
- urldate = {2019-06-20},
- volume = {44},
- year = {2019}
-}
-
-@article{tangaro_laniakea_2020,
- abstract = {AbstractBackground.  While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios wher},
- author = {Tangaro, Marco Antonio and Donvito, Giacinto and Antonacci, Marica and Chiara, Matteo and Mandreoli, Pietro and Pesole, Graziano and Zambelli, Federico},
- doi = {10.1093/gigascience/giaa033},
- journal = {GigaScience},
- keywords = {+Cloud, +Galactic, +IsGalaxy, +RefPublic, {\textgreater}GVL-Unspecified, {\textgreater}Laniakea, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
- language = {en},
- month = {April},
- note = {Publisher: Oxford Academic},
- number = {4},
- shorttitle = {Laniakea},
- title = {Laniakea: an open solution to provide {Galaxy} “on-demand” instances over heterogeneous cloud infrastructures},
- url = {https://academic.oup.com/gigascience/article/9/4/giaa033/5816668},
- urldate = {2020-08-16},
- volume = {9},
- year = {2020}
-}
-
-@article{tari_u2af65_2019,
- abstract = {Abstract The essential splicing factor U2AF65 is known to help anchoring U2 snRNP at the branch site. Its C-terminal UHM domain interacts with ULM motifs of SF3b155, an U2 snRNP protein. Here, we report a cooperative binding of U2AF65 and the related protein CAPERα to the multi-ULM domain of SF3b155. In addition, we show that the RS domain of U2AF65 drives a liquid?liquid phase separation that is amplified by intronic RNA with repeated pyrimidine tracts. In cells, knockdown of either U2AF65 or CAPERα improves the inclusion of cassette exons that are preceded by such repeated pyrimidine-rich motifs. These results support a model in which liquid-like assemblies of U2AF65 and CAPERα on repetitive pyrimidine-rich RNA sequences are driven by their RS domains, and facilitate the recruitment of the multi-ULM domain of SF3b155. We anticipate that posttranslational modifications and proteins recruited in dynamical U2AF65 and CAPERα condensates may further contribute to the complex mechanisms leading to specific splice site choice that occurs in cells.},
- author = {Tari, Manel and Manceau, Valérie and de Matha Salone, Jean and Kobayashi, Asaki and Pastré, David and Maucuer, Alexandre},
- doi = {10.15252/embr.201847604},
- issn = {1469-221X},
- journal = {EMBO reports},
- keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu, RBM39, SF3b1, U2AF2, liquid–liquid phase separation, splicing},
- month = {August},
- number = {8},
- pages = {e47604},
- title = {{U2AF65} assemblies drive sequence-specific splice site recognition},
- url = {https://www.embopress.org/doi/abs/10.15252/embr.201847604},
- urldate = {2019-09-21},
- volume = {20},
- year = {2019}
-}
-
-@article{teikari_insight_2019,
- abstract = {The Baltic Sea is a shallow basin of brackish water in which the spatial salinity gradient is one of the most important factors contributing to species distribution. The Baltic Sea is infamous for its annual cyanobacterial blooms comprised of Nodularia spumigena, Aphanizomenon spp., and Dolichospermum spp. that cause harm, especially for recreational users. To broaden our knowledge of the cyanobacterial adaptation strategies for brackish water environments, we sequenced the entire genome of Dolichospermum sp. UHCC 0315, a species occurring not only in freshwater environments but also in brackish water. Comparative genomics analyses revealed a close association with Dolichospermum sp. UHCC 0090 isolated from a lake in Finland. The genome closure of Dolichospermum sp. UHCC 0315 unraveled a mixture of two subtypes in the original culture, and subtypes exhibited distinct buoyancy phenotypes. Salinity less than 3 g L−1 NaCl enabled proper growth of Dolichospermum sp. UHCC 0315, whereas growth was arrested at moderate salinity (6 g L−1 NaCl). The concentrations of toxins, microcystins, increased at moderate salinity, whereas RNA sequencing data implied that Dolichospermum remodeled its primary metabolism in unfavorable high salinity. Based on our results, the predicted salinity decrease in the Baltic Sea may favor toxic blooms of Dolichospermum spp.},
- author = {Teikari, Jonna E. and Popin, Rafael V. and Hou, Shengwei and Wahlsten, Matti and Hess, Wolfgang R. and Sivonen, Kaarina},
- copyright = {2019 The Author(s)},
- doi = {10.1038/s41598-019-40883-1},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {En},
- month = {March},
- number = {1},
- pages = {4888},
- title = {Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming {Baltic} {Sea} {Dolichospermum} sp. {UHCC} 0315},
- url = {https://www.nature.com/articles/s41598-019-40883-1},
- urldate = {2019-04-06},
- volume = {9},
- year = {2019}
-}
-
-@phdthesis{teixeira_pereira_comprehensive_2020,
- author = {Teixeira Pereira, Bruno Filipe},
- doi = {10.17169/REFUBIUM-26726},
- keywords = {+UsePublic, 500 Natural sciences and mathematics::570 Life sciences::576 Genetics and evolution, {\textgreater}UseGalaxy.eu, Bioinformatics, CRISPR, FOS: Computer and information sciences, Med12, Sall1, lncRNAs, mESCs},
- school = {Freie Universität Berlin},
- title = {A comprehensive analysis of {Med12} controlled (l){ncRNAs} and characterization of a novel {Sall1} antisense transcript},
- type = {{PhD} {Thesis}},
- url = {https://refubium.fu-berlin.de/handle/fub188/26965},
- year = {2020}
-}
-
-@article{tekman_single-cell_2020,
- abstract = {The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets.Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal.The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.},
- author = {Tekman, Mehmet and Batut, Bérénice and Ostrovsky, Alexander and Antoniewski, Christophe and Clements, Dave and Ramirez, Fidel and Etherington, Graham J and Hotz, Hans-Rudolf and Scholtalbers, Jelle and Manning, Jonathan R and Bellenger, Lea and Doyle, Maria A and Heydarian, Mohammad and Huang, Ni and Soranzo, Nicola and Moreno, Pablo and Mautner, Stefan and Papatheodorou, Irene and Nekrutenko, Anton and Taylor, James and Blankenberg, Daniel and Backofen, Rolf and Grüning, Björn},
- doi = {10.1093/gigascience/giaa102},
- issn = {2047-217X},
- journal = {GigaScience},
- keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Human Cell Atlas, {\textgreater}Live EU, {\textgreater}SingleCell},
- month = {October},
- number = {10},
- title = {A single-cell {RNA}-sequencing training and analysis suite using the {Galaxy} framework},
- url = {https://doi.org/10.1093/gigascience/giaa102},
- urldate = {2021-10-03},
- volume = {9},
- year = {2020}
-}
-
-@article{thanki_aequatus:_2018,
- abstract = {Background.  Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, inclu},
- author = {Thanki, Anil S. and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert P.},
- doi = {10.1093/gigascience/giy128},
- journal = {GigaScience},
- keywords = {+Galactic, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {November},
- shorttitle = {Aequatus},
- title = {Aequatus: {An} open-source homology browser},
- url = {https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giy128/5160135},
- urldate = {2018-11-19},
- year = {2018}
-}
-
-@article{torres-paz_maternally_2019,
- abstract = {Sequential developmental events, starting from the moment of fertilization, are crucial for the acquisition of animal body plan. Subtle modifications in such early events are likely to have major impacts in later morphogenesis, bringing along morphological diversification. Here, comparing the blind cave and the surface morphotypes of Astyanax mexicanus fish, we found heterochronies during gastrulation that produce organizer and axial mesoderm tissues with different properties (including differences in the expression of dkk1b) that may have contributed to cavefish brain evolution. These variations observed during gastrulation depend fully on maternal factors. The developmental evolution of retinal morphogenesis and hypothalamic patterning are among those traits that retained significant maternal influence at larval stages. Transcriptomic analysis of fertilized eggs from both morphotypes and reciprocal F1 hybrids showed a strong and specific maternal signature. Our work strongly suggests that maternal effect genes and developmental heterochronies that occur during gastrulation have impacted morphological brain change during cavefish evolution.},
- author = {Torres-Paz, Jorge and Leclercq, Julien and Rétaux, Sylvie},
- doi = {10.7554/eLife.50160},
- editor = {Bronner, Marianne E and Podrabsky, Jason E},
- issn = {2050-084X},
- journal = {eLife},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Astyanax mexicanus, developmental evolution, dkk1b, heterocrhony, maternal transcriptome, prechordal plate},
- month = {October},
- pages = {e50160},
- title = {Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution},
- url = {https://doi.org/10.7554/eLife.50160},
- urldate = {2020-01-04},
- volume = {8},
- year = {2019}
-}
-
-@article{tosar_ri-sec-seq_2021,
- author = {Tosar, Juan and Gámbaro, Fabiana and Castellano, Mauricio and Cayota, Alfonso},
- doi = {10.21769/bioprotoc.3918},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Bio-Protocol, LLC},
- number = {4},
- title = {{RI}-{SEC}-seq: {Comprehensive} {Profiling} of {Nonvesicular} {Extracellular} {RNAs} with {Different} {Stabilities}},
- url = {https://doi.org/10.21769/bioprotoc.3918},
- volume = {11},
- year = {2021}
-}
-
-@article{tu_molecular_2021,
- author = {Tu, Zhiwei and Setlow, Peter and Brul, Stanley and Kramer, Gertjan},
- doi = {10.3390/microorganisms9030667},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- note = {Publisher: MDPI AG},
- number = {3},
- pages = {667},
- title = {Molecular {Physiological} {Characterization} of a {High} {Heat} {Resistant} {Spore} {Forming} {Bacillus} subtilis {Food} {Isolate}},
- url = {https://doi.org/10.3390/microorganisms9030667},
- volume = {9},
- year = {2021}
-}
-
-@article{uellendahl-werth_benchmark_2020,
- abstract = {RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50–80\% unwanted hemoglobin (Hb) transcripts. Lexogen’s QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB’s effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43\% (s.d. 14\%) to 8.0\% (s.d. 4.3\%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8\% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.},
- author = {Uellendahl-Werth, Florian and Wolfien, Markus and Franke, Andre and Wolkenhauer, Olaf and Ellinghaus, David},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-62637-0},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +Shared, +Stellar, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {March},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {1--10},
- title = {A benchmark of hemoglobin blocking during library preparation for {mRNA}-{Sequencing} of human blood samples},
- url = {https://www.nature.com/articles/s41598-020-62637-0},
- urldate = {2020-04-09},
- volume = {10},
- year = {2020}
-}
-
-@article{valsecchi_rna_2020,
- author = {Valsecchi, Claudia Isabelle Keller and Basilicata, M. Felicia and Georgiev, Plamen and Gaub, Aline and Seyfferth, Janine and Kulkarni, Tanvi and Panhale, Amol and Semplicio, Giuseppe and Manjunath, Vinitha and Holz, Herbert and Dasmeh, Pouria and Akhtar, Asifa},
- doi = {10.1038/s41586-020-2935-z},
- journal = {Nature},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {November},
- note = {Publisher: Springer Science and Business Media LLC},
- title = {{RNA} nucleation by {MSL2} induces selective {X} chromosome compartmentalization},
- url = {https://doi.org/10.1038/s41586-020-2935-z},
- year = {2020}
-}
-
-@article{verma_identification_2022,
- author = {Verma, Divya and Bagchi, Preenon and IA, Shylesh Murthy},
- doi = {10.21203/rs.3.rs-1253773/v1},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Research Square Platform LLC},
- title = {Identification {Of} {Taxa} and {Functional} {Pathway} {Information} {Of} {Mycobacterium} tuberculosis {Microbiome} {And} {High} {Throughput} {Simulation} {Studies} {With} {Mycobacteriophage}},
- url = {https://doi.org/10.21203/rs.3.rs-1253773/v1},
- year = {2022}
-}
-
-@article{videm_chira_2021,
- abstract = {With the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated from one of the interaction partners. Owing to short read lengths, often these sequenced arms ambiguously map to multiple locations. Thus, inferring the origin of these can be quite complicated. Here we present ChiRA, a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids.Grouping reference loci on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the selection of the longest hit or a random choice among all hits. On benchmark data ChiRA improved the number of correct alignments to the reference up to 3-fold. It is shown that the genes that belong to the common read loci share the same protein families or similar pathways. In published data, ChiRA could detect 3 times more new interactions compared to existing approaches. In addition, ChiRAViz can be used to visualize and filter large chimeric datasets intuitively.ChiRA tool suite provides a complete analysis and visualization framework along with ready-to-use Galaxy workflows and tutorials for RNA-RNA interactome and structurome datasets. Common read loci built by ChiRA can rescue multi-mapped reads on paralogous genes without requiring any information on gene relations. We showed that ChiRA is sensitive in detecting new RNA-RNA interactions from published RNA-RNA interactome datasets.},
- author = {Videm, Pavankumar and Kumar, Anup and Zharkov, Oleg and Grüning, Björn Andreas and Backofen, Rolf},
- doi = {10.1093/gigascience/giaa158},
- issn = {2047-217X},
- journal = {GigaScience},
- keywords = {+Education, +Galactic, +Shared, +Tools, {\textgreater}RNA Workbench},
- month = {February},
- number = {giaa158},
- shorttitle = {{ChiRA}},
- title = {{ChiRA}: an integrated framework for chimeric read analysis from {RNA}-{RNA} interactome and {RNA} structurome data},
- url = {https://doi.org/10.1093/gigascience/giaa158},
- urldate = {2021-03-08},
- volume = {10},
- year = {2021}
-}
-
-@article{villa_data_2021,
- abstract = {Pervasive transcription originating from the ubiquitous activity of RNA Polymerase II (RNAPII) generates a vast mass of non-coding RNAs (ncRNAs) that represent a potential harm to gene expression. In the compact genome of the yeast Saccharomyces cerevisiae, the main genomewide safeguard against pervasive ncRNAs is the Nrd1-Nab3-Sen1 (NNS) complex, composed of two RNA-binding proteins (Nrd1 and Nab3) and the helicase Sen1. The NNS complex directs transcription termination of ncRNA genes and promotes the rapid degradation of pervasive transcripts from yeast nuclei through its physical and functional coupling to the nuclear RNA exosome. We have recently shown that inhibition of the exosome in yeast cells leads to the accumulation of ncRNAs complexed with Nab3 and Nrd1, decreasing recycling of these termination factors to sites of transcription and inducing global termination defects at NNS targets. Consistent with the notion that ncRNAs out-titrate Nab3 and Nrd1 termination factors, we have shown that a similar genomewide termination impairment could be achieved by expressing a circular RNA decoy containing a Nab3 binding target [1]. In relation to this previous research article, here we expand our observations on the effect of the circular RNA decoy on NNS termination. We aimed at verifying that the Nab3 binding sequence present on the decoy is indeed efficiently sequestering Nab3 as intended by design, leading to the expected decrease of Nab3 binding on NNS targets. We employed the crosslinking and cDNA analysis protocol (CRAC) on yeast cells expressing the circular ncRNA decoy or a control construct. We present data from high-resolution genomewide RNA binding of Nab3 in three independent biological replicates of these S.cerevisiae cells, normalized by spiked-in S.pombe lysates. These data allow the useful assessment of the extent of co-transcriptional binding decrease of Nab3 by decoy ncRNA titration and will be valuable for further analyses of NNS targeting mechanisms.},
- author = {Villa, Tommaso and Jaszczyszyn, Yan and Libri, Domenico},
- doi = {10.1016/j.dib.2021.106951},
- issn = {2352-3409},
- journal = {Data in Brief},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}deepTools, CRAC, Circular RNA, Cryptic unstable transcripts, Non-coding RNAs, Nrd1-Nab3-Sen1 (NNS) complex, Pervasive transcription, Transcription termination, Yeast},
- language = {en},
- month = {April},
- pages = {106951},
- title = {Data from crosslinking and analysis of {cDNAs} ({CRAC}) of {Nab3} in yeast cells expressing a circular {ncRNA} decoy},
- url = {https://www.sciencedirect.com/science/article/pii/S2352340921002353},
- urldate = {2021-08-19},
- volume = {35},
- year = {2021}
-}
-
-@article{villa_degradation_2020,
- abstract = {A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. Here, we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, circular RNA containing a natural NNS target in exosome-proficient cells. Our results have important implications for the mechanism of termination, the general impact of ncRNAs abundance, and the importance of nuclear ncRNA degradation.},
- author = {Villa, Tommaso and Barucco, Mara and Martin-Niclos, Maria-Jose and Jacquier, Alain and Libri, Domenico},
- doi = {10.1016/j.celrep.2020.107942},
- issn = {2211-1247},
- journal = {Cell Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}ABiMS, {\textgreater}UseGalaxy.eu, NNS complex, Nrd1-Nab3-Sen1 complex, Rrp6, cryptic unstable transcripts, exosome, non-coding RNAs, pervasive transcription, transcription termination, yeast Saccharomyces cerevisiae},
- language = {en},
- month = {July},
- number = {3},
- pages = {107942},
- title = {Degradation of {Non}-coding {RNAs} {Promotes} {Recycling} of {Termination} {Factors} at {Sites} of {Transcription}},
- url = {http://www.sciencedirect.com/science/article/pii/S2211124720309232},
- urldate = {2020-08-13},
- volume = {32},
- year = {2020}
-}
-
-@article{voelker_high-quality_2021,
- author = {Voelker, Julia and Shepherd, Mervyn and Mauleon, Ramil},
- doi = {10.46471/gigabyte.28},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {Publisher: GigaScience Press},
- pages = {1--15},
- title = {A high-quality draft genome for {Melaleuca} alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species},
- url = {https://doi.org/10.46471/gigabyte.28},
- volume = {2021},
- year = {2021}
-}
-
-@article{volkova_radiosensitivity_2021,
- author = {Volkova, Polina Yu and Duarte, Gustavo T. and Kazakova, Elizaveta A. and Makarenko, Ekaterina S. and Bitarishvili, Sofia V. and Bondarenko, Vladimir S. and Perevolotskii, Alexander N. and Geras'kin, Stanislav A. and Garbaruk, Dmitrii K. and Turchin, Larisa M.},
- doi = {10.1016/j.scitotenv.2021.146206},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Elsevier BV},
- pages = {146206},
- title = {Radiosensitivity of herbaceous plants to chronic radiation exposure: {Field} study in the {Chernobyl} exclusion zone},
- url = {https://doi.org/10.1016/j.scitotenv.2021.146206},
- volume = {777},
- year = {2021}
-}
-
-@incollection{von_suchodoletz_lessons_2020,
- author = {Von Suchodoletz, Dirk and Bauer, Jonathan and Zharkov, Oleg},
- booktitle = {E-{Science}-{Tage} 2019},
- keywords = {+RefPublic, {\textgreater}UseGalaxy.eu},
- language = {eng},
- note = {Version Number: 1},
- publisher = {University Library Heidelberg},
- title = {Lessons learned from {Virtualized} {Research} {Environments} in today’s scientific compute infrastructures},
- url = {https://books.ub.uni-heidelberg.de/index.php/heibooks/catalog/book/598/c8418},
- urldate = {2020-05-27},
- year = {2020}
-}
-
-@article{weigang_within-host_2021,
- author = {Weigang, Sebastian and Fuchs, Jonas and Zimmer, Gert and Schnepf, Daniel and Kern, Lisa and Beer, Julius and Luxenburger, Hendrik and Ankerhold, Jakob and Falcone, Valeria and Kemming, Janine and Hofmann, Maike and Thimme, Robert and Neumann-Haefelin, Christoph and Ulferts, Svenja and Grosse, Robert and Hornuss, Daniel and Tanriver, Yakup and Rieg, Siegbert and Wagner, Dirk and Huzly, Daniela and Schwemmle, Martin and Panning, Marcus and Kochs, Georg},
- doi = {10.1101/2021.04.30.21256244},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {May},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {Within-host evolution of {SARS}-{CoV}-2 in an immunosuppressed {COVID}-19 patient: a source of immune escape variants},
- url = {https://doi.org/10.1101/2021.04.30.21256244},
- year = {2021}
-}
-
-@article{weise_foxg1_2018,
- abstract = {Rett syndrome is a complex neurodevelopmental disorder that is mainly caused by mutations in MECP2. However, mutations in FOXG1 cause a less frequent form of atypical Rett syndrome, called FOXG1 syndrome. FOXG1 is a key transcription factor crucial for forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Using genome-wide small RNA sequencing and quantitative proteomics, we identified that FOXG1 affects the biogenesis of miR200b/a/429 and interacts with the ATP-dependent RNA helicase, DDX5/p68. Both FOXG1 and DDX5 associate with the microprocessor complex, whereby DDX5 recruits FOXG1 to DROSHA. RNA-Seq analyses of Foxg1cre/+ hippocampi and N2a cells overexpressing miR200 family members identified cAMP-dependent protein kinase type II-beta regulatory subunit (PRKAR2B) as a target of miR200 in neural cells. PRKAR2B inhibits postsynaptic functions by attenuating protein kinase A (PKA) activity; thus, increased PRKAR2B levels may contribute to neuronal dysfunctions in FOXG1 syndrome. Our data suggest that FOXG1 regulates PRKAR2B expression both on transcriptional and posttranscriptional levels.},
- author = {Weise, Stefan C. and Arumugam, Ganeshkumar and Villarreal, Alejandro and Videm, Pavankumar and Heidrich, Stefanie and Nebel, Nils and Dumit, Verónica I. and Sananbenesi, Farahnaz and Reimann, Viktoria and Craske, Madeline and Schilling, Oliver and Hess, Wolfgang R. and Fischer, Andre and Backofen, Rolf and Vogel, Tanja},
- doi = {10.1007/s12035-018-1444-7},
- issn = {1559-1182},
- journal = {Molecular Neurobiology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Atypical Rett syndrome, DROSHA, MECP2, Neurogenesis, PKA},
- language = {en},
- month = {December},
- title = {{FOXG1} {Regulates} {PRKAR2B} {Transcriptionally} and {Posttranscriptionally} via {miR200} in the {Adult} {Hippocampus}},
- url = {https://doi.org/10.1007/s12035-018-1444-7},
- urldate = {2019-01-23},
- year = {2018}
-}
-
-@article{werner_mitochondrial_2022,
- author = {Werner, Erica and Gokhale, Avanti and Ackert, Molly and Xu, Chongchong and Wen, Zhexing and Roberts, Anne M and Roberts, Blaine R and Vrailas-Mortimer, Alysia R and Crocker, Amanda J and Faundez, Victor},
- journal = {bioRxiv},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- note = {Publisher: Cold Spring Harbor Laboratory},
- title = {The {Mitochondrial} {RNA} {Granule} is {Necessary} for {Parkinsonism}-{Associated} {Metal} {Toxicity}},
- year = {2022}
-}
-
-@article{weterings_duration_2021,
- abstract = {Background Escherichia coli sequence type ST131 is a recently emerged worldwide pandemic clonal group. Antibiotic resistance, virulence factors or colonisation fitness are mentioned among other as possible factors contributing to the worldwide success. In this study, we assessed the duration of rectal ESBL- producing E. coli colonisation in the residents, and compare duration of colonisation for ESBL-ST131 versus ESBL-non-ST131.MethodsRectal or faecal samples were obtained from residents of nursing home A between 2013 and 2019 and nursing home B between 2017 and 2019, with repeated point prevalence surveys at intervals of three to six months. Extended-spectrum β-lactamase (ESBL)-producing strains of E. coli were identified on selective culture and selective\ enrichment\ broth, and examined by antimicrobial susceptibility testing. In nursing home A multilocus sequence typing (MLST) and cluster analyse was performed by respectively O25:ST131-specific PCR and amplified fragment length polymorphism (AFLP). In nursing home B whole genome sequencing data were used to determine MLST and to perform a cluster analyse. Kaplan Meier survival analysis was performed to calculate the median time of rectal colonisation of ESBL-EC with a Log-Rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131.ResultsA total of 144 residents were included: 84 residents (58\%) with ESBL-ST131 rectal colonisation and 60 residents (42\%) with ESBL-non-ST131 rectal colonisation. Survival analysis showed a median colonisation length of 13 months for ESBL-ST131 (95\%CI: 7,2 – 18,7) versus 8,3 months (95\%CI: 2,8 – 13,8) for ESBL-non-ST131 (p = 0,028). Remarkably, in the subgroup ST131 the median colonisation length was significantly longer in female than in males: 25,7 months versus 8,1 months (p = 0,013).ConclusionHere we found a prolonged colonisation duration of ESBL-ST131 compared to ESBL-non-ST131 in residents of Dutch nursing homes. Prolonged colonisation duration complicates the controlling and ending an ESBL-ST131 outbreak, especially in long stay settings such as nursing homes.\ },
- author = {Weterings, Veronica and Goede, Tineke de and Hendriks, Yvonne and Kilsdonk, Linda and Mulders, Ans and Wier, Bregje van de and Kluytmans, Jan},
- doi = {10.21203/rs.3.rs-136458/v1},
- journal = {Research Square},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- month = {August},
- note = {ISSN: 2693-5015
-Type: article},
- shorttitle = {Duration of {Colonisation} {With} {Extended}-spectrum {Beta}-lactamase-producing {Escherichia} {Coli}},
- title = {Duration of {Colonisation} {With} {Extended}-spectrum {Beta}-lactamase-producing {Escherichia} {Coli}: {Results} of an {Open} {Cohort} {Study} {With} {Dutch} {Nursing} {Home} {Residents} (2013 – 2019)},
- url = {https://www.researchsquare.com/article/rs-136458/v1},
- urldate = {2021-08-24},
- year = {2021}
-}
-
-@article{wibberg_nbi_2019,
- abstract = {The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR network. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training \& Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 250 training courses were carried out with more than 5,200 participants and these courses received recommendation rates of almost 90\% (status as of October 2019). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.},
- author = {Wibberg, Daniel and Batut, Bérénice and Belmann, Peter and Blom, Jochen and Glöckner, Frank Oliver and Grüning, Björn and Hoffmann, Nils and Kleinbölting, Nils and Rahn, René and Rey, Maja and Scholz, Uwe and Sharan, Malvika and Tauch, Andreas and Trojahn, Ulrike and Usadel, Björn and Kohlbacher, Oliver},
- doi = {10.12688/f1000research.20244.2},
- issn = {2046-1402},
- journal = {F1000Research},
- keywords = {+Education, +Galactic, +RefPublic, {\textgreater}RNA Workbench, {\textgreater}Street Science, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {November},
- pages = {1877},
- title = {The de.{NBI} / {ELIXIR}-{DE} training platform - {Bioinformatics} training in {Germany} and across {Europe} within {ELIXIR}},
- url = {https://f1000research.com/articles/8-1877/v2},
- urldate = {2019-11-27},
- volume = {8},
- year = {2019}
-}
-
-@article{wichers_common_2021,
- author = {Wichers, J. Stephan and Tonkin-Hill, Gerry and Thye, Thorsten and Krumkamp, Ralf and Kreuels, Benno and Strauss, Jan and Thien, Heidrun von and Scholz, Judith AM and Hansson, Helle Smedegaard and Jensen, Rasmus Weisel and Turner, Louise and Lorenz, Freia-Raphaella and Schöllhorn, Anna and Bruchhaus, Iris and Tannich, Egbert and Fendel, Rolf and Otto, Thomas D. and Lavstsen, Thomas and Gilberger, Tim W. and Duffy, Michael F. and Bachmann, Anna},
- doi = {10.7554/elife.69040},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: eLife Sciences Publications, Ltd},
- title = {Common virulence gene expression in adult first-time infected malaria patients and severe cases},
- url = {https://doi.org/10.7554/elife.69040},
- volume = {10},
- year = {2021}
-}
-
-@article{winkler_contrast_2020,
- abstract = {Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differentialmass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficientdiscovery of ‘regions of interest’ (ROI) is of utmost importance in MSI. However, often the discovery of ROIs is hampered by high background noise and artifact signals. Especially in ambient ionization MSI, unmasking biologically relevant information from crude data sets is challenging. Therefore, we implemented a Threshold Intensity Quantization (TrIQ) algorithm for augmenting the contrast in MSI data visualizations. The simple algorithm reduces the impact of extreme values (‘outliers’) and rescales the dynamic range of mass signals. We provide an R script for post-processing MSI data in the imzML community format (https://bitbucket.org/lababi/msi.r) and implemented the TrIQ in our open-source imaging software RmsiGUI (https://bitbucket.org/lababi/rmsigui/). Applying these programs to different biological MSI data sets demonstrated the universal applicability of TrIQ for improving the contrast in the MSI data visualization. We show that TrIQ improves a subsequent detection of ROIs by sectioning. In addition, the adjustment of the dynamic signal intensity range makes MSI data sets comparable.},
- author = {Winkler, Robert and Rosas-Román, Ignacio},
- doi = {10.26434/chemrxiv.12312251.v1},
- journal = {ChemRxiv},
- keywords = {+RefPublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: ChemRxiv},
- title = {Contrast {Optimization} of {Mass} {Spectrometry} {Imaging} ({MSI}) {Data} {Visualization} by {Threshold} {Intensity} {Quantization} ({TrIQ})},
- url = {https://chemrxiv.org/articles/preprint/Contrast_Optimization_of_Mass_Spectrometry_Imaging_MSI_Data_Visualization_by_Threshold_Intensity_Quantization_TrIQ_/12312251},
- urldate = {2020-08-13},
- year = {2020}
-}
-
-@article{winkler_gene_2021,
- author = {Winkler, Martin A. and Pan, Alfred A.},
- doi = {10.21203/rs.3.rs-553828/v2},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {July},
- note = {Publisher: Research Square Platform LLC},
- title = {Gene {Homologies} {Identified} between {Trypanosoma} cruzi {Antigen} 36 and {Mammalian} {TRIM21} {Genes} {Using} {Bioinformatics} {Analysis}},
- url = {https://doi.org/10.21203/rs.3.rs-553828/v2},
- year = {2021}
-}
-
-@article{wirth_characterization_2019,
- abstract = {Microalgal biomass is an alternative feedstock for biogas production although its C/N ratio is usually lower than optimal, therefore co-fermentation is recommended. Identification of the core microbiome by metagenome analysis and prediction of functional characteristics are essential to make microalgal feedstock more sustainable and economically feasible. Biogas production from photoautotrophically grown Chlorella vulgaris (Ch. vulgaris) biomass (240 mL CH4 g oTS-1) and co-fermentation with maize silage (330 mL CH4 g oTS-1) has been studied in semi continuous laboratory biogas fermenters. Maize silage control yielded 310 mL CH4 g oTS-1. The microbial community and the read-based functional profiles, derived from these data, were examined during the process by using next-generation metagenome Ion Torrent sequencing technology. The read-based core microbiome consisted of 92 genera from which 60 abundant taxa were directly associated with the microbial methane producing food chain. The data-set was also analyzed in a genome-based approach. 65 bins were assembled, 52 of them belonged in the core biogas producing genera identified by the read-based metagenomes. The read-based and genome-based approaches complemented and verified each other. The functional profiles indicated a variety of glycoside hydrolases. Substantial rearrangements of the methanogen functions have also been observed. Co-fermentation of algal biomass and plant biomass can be carried out for an extended period of time without process failure. The microbial members of the inoculum are well conserved, feedstock composition cause relative abundance changes in the core microbiome.},
- author = {Wirth, Roland and Böjti, Tamás and Lakatos, Gergely and Maróti, Gergely and Bagi, Zoltán and Rákhely, Gábor and Kovács, Kornél L.},
- doi = {10.3389/fenrg.2019.00111},
- issn = {2296-598X},
- journal = {Frontiers in Energy Research},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Co-fermentation, Metagenome, binning, biogas, core microbiome, functional characteristcs, microalgae},
- language = {English},
- title = {Characterization of {Core} {Microbiomes} and {Functional} {Profiles} of {Mesophilic} {Anaerobic} {Digesters} {Fed} {With} {Chlorella} vulgaris {Green} {Microalgae} and {Maize} {Silage}},
- url = {https://www.frontiersin.org/articles/10.3389/fenrg.2019.00111/full},
- urldate = {2019-11-25},
- volume = {7},
- year = {2019}
-}
-
-@article{wirth_chlorella_2020,
- abstract = {Microalgae-based bioenergy production is a promising field with regard to the wide variety of algal species and metabolic potential. The use of liquid wastes as nutrient clearly improves the sustainability of microalgal biofuel production. Microalgae and bacteria have an ecological inter-kingdom relationship. This microenvironment called phycosphere has a major role in the ecosystem productivity and can be utilized both in bioremediation and biomass production. However, knowledge on the effects of indigenous bacteria on microalgal growth and the characteristics of bacterial communities associated with microalgae are limited. In this study municipal, industrial and agricultural liquid waste derivatives were used as cultivation media. Chlorella vulgaris green microalgae and its bacterial partners efficiently metabolized the carbon, nitrogen and phosphorous content available in these wastes. The read-based metagenomics approach revealed a diverse microbial composition at the start point of cultivations in the different types of liquid wastes. The relative abundance of the observed taxa significantly changed over the cultivation period. The genome-centric reconstruction of phycospheric bacteria further explained the observed correlations between the taxonomic composition and biomass yield of the various waste-based biodegradation systems. Functional profile investigation of the reconstructed microbes revealed a variety of relevant biological processes like organic acid oxidation and vitamin B synthesis. Thus, liquid wastes were shown to serve as valuable resources of nutrients as well as of growth promoting bacteria enabling increased microalgal biomass production.},
- author = {Wirth, Roland and Pap, Bernadett and Böjti, Tamás and Shetty, Prateek and Lakatos, Gergely and Bagi, Zoltán and Kovács, Kornél L. and Maróti, Gergely},
- doi = {10.3389/fbioe.2020.557572},
- issn = {2296-4185},
- journal = {Frontiers in Bioengineering and Biotechnology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Metagenomics, algal-bacterial interactions, green algae, phycosphere, wastewater},
- language = {English},
- note = {Publisher: Frontiers},
- shorttitle = {Chlorella vulgaris and {Its} {Phycosphere} in {Wastewater}},
- title = {Chlorella vulgaris and {Its} {Phycosphere} in {Wastewater}: {Microalgae}-{Bacteria} {Interactions} {During} {Nutrient} {Removal}},
- url = {https://www.frontiersin.org/articles/10.3389/fbioe.2020.557572/full},
- urldate = {2021-01-08},
- volume = {8},
- year = {2020}
-}
-
-@article{witmer_epigenetic_2020,
- abstract = {The malaria parasite replicates asexually in the red blood cells of its vertebrate host employing epigenetic mechanisms to regulate gene expression in response to changes in its environment. We used chromatin immunoprecipitation followed by sequencing in conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental transition from asexual blood stages to male and female gametocytes and to ookinetes in the rodent malaria parasite Plasmodium berghei. Across the developmental stages examined, heterochromatin protein 1 associates with variantly expressed gene families localised at subtelomeric regions and variant gene expression based on heterochromatic silencing is observed only in some genes. Conversely, the euchromatin mark histone 3 lysine 9 acetylation (H3K9ac) is abundant in non-heterochromatic regions across all developmental stages. H3K9ac presents a distinct pattern of enrichment around the start codon of ribosomal protein genes in all stages but male gametocytes. Additionally, H3K9ac occupancy positively correlates with transcript abundance in all stages but female gametocytes suggesting that transcription in this stage is independent of H3K9ac levels. This finding together with known mRNA repression in female gametocytes suggests a multilayered mechanism operating in female gametocytes in preparation for fertilization and zygote development, coinciding with parasite transition from host to vector.},
- author = {Witmer, Kathrin and Fraschka, Sabine A. and Vlachou, Dina and Bártfai, Richárd and Christophides, George K.},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-63121-5},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {April},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {6354},
- title = {An epigenetic map of malaria parasite development from host to vector},
- url = {https://www.nature.com/articles/s41598-020-63121-5},
- urldate = {2020-05-20},
- volume = {10},
- year = {2020}
-}
-
-@article{wolf_comparative_2021,
- abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods{\textless}/h3{\textgreater} {\textless}p{\textgreater}The present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Transcriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size \textit{in vivo}.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Funding{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study was funded by the Helmut-Ecker-Stiftung and the Volker-Homann-Stiftung.{\textless}/p{\textgreater}},
- author = {Wolf, Julian and Schlecht, Anja and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Lange, Clemens},
- copyright = {© 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
- doi = {10.1101/2021.05.10.443381},
- journal = {bioRxiv},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {May},
- note = {Publisher: Cold Spring Harbor Laboratory
-Section: New Results},
- pages = {2021.05.10.443381},
- title = {Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration},
- url = {https://www.biorxiv.org/content/10.1101/2021.05.10.443381v1},
- urldate = {2021-07-27},
- year = {2021}
-}
-
-@article{wolf_comparative_2022,
- author = {Wolf, Julian and Schlecht, Anja and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Lange, Clemens},
- doi = {10.1016/j.bbadis.2022.166340},
- journal = {Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {April},
- note = {Publisher: Elsevier BV},
- number = {4},
- pages = {166340},
- title = {Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration},
- url = {https://doi.org/10.1016/j.bbadis.2022.166340},
- volume = {1868},
- year = {2022}
-}
-
-@article{wolf_corneal_2020,
- abstract = {Purpose
-Immune reactions following corneal transplantation are the most common cause of transplant failure. However, the underlying mechanisms of corneal graft rejection are not yet fully understood but increasing evidence points to a crucial role of the innate immune system in this context. Using a human in vitro model, we aimed to assess the response of human macrophages to stimulation with human corneal tissue and whether corneal endothelial cells (CEC) have immune-modulating properties.
-Methods
-Human monocytes were isolated from peripheral blood mononuclear cells and differentiated into monocyte-derived macrophages (MDM). A standardized protocol was used for disaggregation of human corneas into fragments of defined sizes. MDMs were stimulated using processed corneal material with or without CEC. Lipopolysaccharide (LPS) or interferon-gamma (IFNγ) served as controls. RNA sequencing was applied to analyze the impact of differential stimulation of MDMs on their transcriptional profile. RNA sequencing results were validated using digital PCR.
-Results
-The transcriptional profile of MDMs was significantly modulated by the type of stimulus used for MDM activation as well as by the individual MDM donor. LPS- or IFNγ-stimulation resulted in distinct transcriptional alterations compared to unstimulated MDMs including an upregulation of various cytokines such as CCL3, 4, 5, 19 or CXCL9. Corneal tissue induced the differential expression of 45 genes when compared to unstimulated MDMs, with several metallothioneins (MTs) among the upregulated factors (MT1A, MT1E, MT1F, MT1G, MT1H, MT1L, MT1M, MT1X, MT2A). This effect was independent of the presence or absence of CEC. PCR validation confirmed induction of 3 different metallothioneins (MT1G, MT1H and MT2A) in MDMs stimulated by corneal tissue.
-Conclusions
-The MDM in vitro model proved to be a robust tool to study the effects of LPS, IFNγ and corneal tissue homogenates on the transcriptional activity of MDM. Human macrophages showed a distinct upregulation of various MTs when challenged with human corneal allogen with or without corneal endothelium, which might have an immune-modulatory effect. As a general observation, it appears that in MDM-based studies a significant donor-dependent effect on the transcriptional profile of MDMs needs to be considered and adjusted before downstream analysis.},
- author = {Wolf, Julian and Zhuang, Xinyu and Hildebrand, Antonia and Boneva, Stefaniya and Schwämmle, Melanie and Kammrath Betancor, Paola and Fan, Jiaqi and Böhringer, Daniel and Maier, Philip and Lange, Clemens and Reinhard, Thomas and Schlunck, Günther and Lapp, Thabo},
- doi = {10.1016/j.molimm.2020.10.016},
- issn = {0161-5890},
- journal = {Molecular Immunology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Corneal endothelial cells, Corneal graft rejection, MDM, Macrophage, RNA sequencing},
- language = {en},
- month = {December},
- pages = {188--194},
- title = {Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages},
- url = {http://www.sciencedirect.com/science/article/pii/S0161589020305216},
- urldate = {2021-01-13},
- volume = {128},
- year = {2020}
-}
-
-@article{wolf_human_2022,
- author = {Wolf, Julian and Boneva, Stefaniya and Schlecht, Anja and Lapp, Thabo and Auw-Haedrich, Claudia and Lagrèze, Wolf and Agostini, Hansjürgen and Reinhard, Thomas and Schlunck, Günther and Lange, Clemens},
- doi = {10.1016/j.ygeno.2022.110286},
- journal = {Genomics},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {February},
- note = {Publisher: Elsevier BV},
- pages = {110286},
- title = {The {Human} {Eye} {Transcriptome} {Atlas}: {A} searchable comparative transcriptome database for healthy and diseased human eye tissue},
- url = {https://doi.org/10.1016/j.ygeno.2022.110286},
- year = {2022}
-}
-
-@article{wolf_transcriptional_2020,
- abstract = {This study characterizes the transcriptome and the cellular tumor microenvironment (TME) of conjunctival melanoma (CM) and identifies prognostically relevant biomarkers. 12 formalin-fixed and paraffin-embedded CM were analyzed by MACE RNA sequencing, including six cases each with good or poor clinical outcome, the latter being defined by local recurrence and/or systemic metastases. Eight healthy conjunctival specimens served as controls. The TME of CM, as determined by bioinformatic cell type enrichment analysis, was characterized by the enrichment of melanocytes, pericytes and especially various immune cell types, such as plasmacytoid dendritic cells, natural killer T cells, B cells and mast cells. Differentially expressed genes between CM and control were mainly involved in inhibition of apoptosis, proteolysis and response to growth factors. POU3F3, BIRC5 and 7 were among the top expressed genes associated with inhibition of apoptosis. 20 genes, among them CENPK, INHA, USP33, CASP3, SNORA73B, AAR2, SNRNP48 and GPN1, were identified as prognostically relevant factors reaching high classification accuracy (area under the curve: 1.0). The present study provides new insights into the TME and the transcriptional profile of CM and additionally identifies new prognostic biomarkers. These results add new diagnostic tools and may lead to new options of targeted therapy for CM.},
- author = {Wolf, Julian and Auw-Haedrich, Claudia and Schlecht, Anja and Boneva, Stefaniya and Mittelviefhaus, Hans and Lapp, Thabo and Agostini, Hansjürgen and Reinhard, Thomas and Schlunck, Günther and Lange, Clemens A. K.},
- copyright = {2020 The Author(s)},
- doi = {10.1038/s41598-020-72864-0},
- issn = {2045-2322},
- journal = {Scientific Reports},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {October},
- note = {Number: 1
-Publisher: Nature Publishing Group},
- number = {1},
- pages = {17022},
- title = {Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures},
- url = {https://www.nature.com/articles/s41598-020-72864-0},
- urldate = {2021-05-15},
- volume = {10},
- year = {2020}
-}
-
-@article{wolff_galaxy_2018,
- abstract = {Abstract.  Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visu},
- author = {Wolff, Joachim and Bhardwaj, Vivek and Nothjunge, Stephan and Richard, Gautier and Renschler, Gina and Gilsbach, Ralf and Manke, Thomas and Backofen, Rolf and Ramírez, Fidel and Grüning, Björn A.},
- doi = {10.1093/nar/gky504},
- issn = {0305-1048},
- journal = {Nucleic Acids Research},
- keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}HiCExplorer, {\textgreater}UseGalaxy.eu},
- language = {en},
- month = {July},
- number = {W1},
- pages = {W11--W16},
- shorttitle = {Galaxy {HiCExplorer}},
- title = {Galaxy {HiCExplorer}: a web server for reproducible {Hi}-{C} data analysis, quality control and visualization},
- url = {https://academic.oup.com/nar/article/46/W1/W11/5036837},
- urldate = {2018-07-18},
- volume = {46},
- year = {2018}
-}
-
-@incollection{wolfien_single-cell_2021,
- author = {Wolfien, Markus and David, Robert and Galow, Anne-Marie},
- doi = {10.36255/exonpublications.bioinformatics.2021.ch2},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {March},
- pages = {19--35},
- publisher = {Exon Publications},
- title = {Single-{Cell} {RNA} {Sequencing} {Procedures} and {Data} {Analysis}},
- url = {https://doi.org/10.36255/exonpublications.bioinformatics.2021.ch2},
- year = {2021}
-}
-
-@incollection{wolfien_workflow_2019,
- abstract = {During the last decade, ncRNAs have been investigated intensively and revealed their regulatory role in various biological processes. Worldwide research efforts have identified numerous ncRNAs and multiple RNA subtypes, which are attributed to diverse functionalities known to interact with different functional layers, from DNA and RNA to proteins. This makes the prediction of functions for newly identified ncRNAs challenging. Current bioinformatics and systems biology approaches show promising results to facilitate an identification of these diverse ncRNA functionalities. Here, we review (a) current experimental protocols, i.e., for Next Generation Sequencing, for a successful identification of ncRNAs; (b) sequencing data analysis workflows as well as available computational environments; and (c) state-of-the-art approaches to functionally characterize ncRNAs, e.g., by means of transcriptome-wide association studies, molecular network analyses, or artificial intelligence guided prediction. In addition, we present a strategy to cover the identification and functional characterization of unknown transcripts by using connective workflows.},
- address = {New York, NY},
- author = {Wolfien, Markus and Brauer, David Leon and Bagnacani, Andrea and Wolkenhauer, Olaf},
- booktitle = {Computational {Biology} of {Non}-{Coding} {RNA}: {Methods} and {Protocols}},
- doi = {10.1007/978-1-4939-8982-9_5},
- editor = {Lai, Xin and Gupta, Shailendra K. and Vera, Julio},
- isbn = {978-1-4939-8982-9},
- keywords = {+Other, +RefPublic, {\textgreater}RNA Workbench, Co-expression analysis, Data analysis, Experimental RNA discovery, Machine learning, Network analysis, Next Generation Sequencing, Transcript identification, Workflow, ncRNA},
- language = {en},
- pages = {111--132},
- publisher = {Springer New York},
- series = {Methods in {Molecular} {Biology}},
- title = {Workflow {Development} for the {Functional} {Characterization} of {ncRNAs}},
- url = {https://doi.org/10.1007/978-1-4939-8982-9_5},
- urldate = {2019-01-25},
- year = {2019}
-}
-
-@article{wright*_structure_2018,
- abstract = {Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in “wet” laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also briefly mention recent advances in whole-genome interactomics and how this may influence the field of predictive RNA research.},
- author = {Wright*, Patrick R. and Mann*, Martin and Backofen*, Rolf},
- doi = {10.1128/microbiolspec.RWR-0001-2017},
- issn = {2165-0497},
- journal = {Microbiology Spectrum},
- keywords = {+RefPublic, +Workbench, {\textgreater}RNA Workbench},
- language = {en},
- month = {April},
- number = {2},
- title = {Structure and {Interaction} {Prediction} in {Prokaryotic} {RNA} {Biology}},
- url = {http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.RWR-0001-2017},
- urldate = {2018-04-28},
- volume = {6},
- year = {2018}
-}
-
-@article{wylie_whole-genome_2019,
- abstract = {Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100\% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.},
- author = {Wylie, Kristine M. and Wylie, Todd N. and Minx, Patrick J. and Rosen, David A.},
- doi = {10.3389/fcimb.2019.00014},
- issn = {2235-2988},
- journal = {Frontiers in Cellular and Infection Microbiology},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella  pneumoniae, Strain tracking, Urinary tract infection (UTI), single nucleotide variants (SNVs), whole genome   sequencing},
- language = {English},
- title = {Whole-{Genome} {Sequencing} of {Klebsiella} pneumoniae {Isolates} to {Track} {Strain} {Progression} in a {Single} {Patient} {With} {Recurrent} {Urinary} {Tract} {Infection}},
- url = {https://www.frontiersin.org/articles/10.3389/fcimb.2019.00014/full},
- urldate = {2019-03-24},
- volume = {9},
- year = {2019}
-}
-
-@article{yanta_cryptogenotyper_2021,
- abstract = {Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3\% (428/431) and 95.1\% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6\% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.},
- author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.},
- doi = {10.1016/j.fawpar.2021.e00115},
- issn = {2405-6766},
- journal = {Food and Waterborne Parasitology},
- keywords = {+Stellar, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}VEuPathDB, Genotyping tool, Mixed infections, SSU rRNA gene, Sanger sequencing, Validated database, gene},
- language = {en},
- month = {June},
- pages = {e00115},
- shorttitle = {{CryptoGenotyper}},
- title = {{CryptoGenotyper}: {A} new bioinformatics tool for rapid {Cryptosporidium} identification},
- url = {https://www.sciencedirect.com/science/article/pii/S2405676621000068},
- urldate = {2021-08-19},
- volume = {23},
- year = {2021}
-}
-
-@article{yol_high-density_2021,
- author = {Yol, Engin and Basak, Merve and Kızıl, Sibel and Lucas, Stuart James and Uzun, Bulent},
- doi = {10.3389/fpls.2021.679659},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: Frontiers Media SA},
- title = {A {High}-{Density} {SNP} {Genetic} {Map} {Construction} {Using} {ddRAD}-{Seq} and {Mapping} of {Capsule} {Shattering} {Trait} in {Sesame}},
- url = {https://doi.org/10.3389/fpls.2021.679659},
- volume = {12},
- year = {2021}
-}
-
-@article{yoshida_dataset_2020,
- abstract = {In this article, we report the first de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus. In this data, 75,320,390 raw reads were acquired from African bullfrog mRNA using Illumina paired-end sequencing platform. De novo assembly resulted in a total of 136,958 unigenes. In the obtained unigenes, 30,039 open reading frames (ORFs) were detected. This dataset provides basic information for molecular level analysis of this species, which undergoes a state of dormancy under dry conditions at ordinary temperatures called estivation.},
- author = {Yoshida, Naoki and Kaito, Chikara},
- doi = {10.1016/j.dib.2020.105388},
- issn = {2352-3409},
- journal = {Data in Brief},
- keywords = {+Methods, +UsePublic, {\textgreater}RNA Workbench, African bullfrog, RNA-Seq, Transcriptome, assembly},
- language = {en},
- month = {June},
- pages = {105388},
- title = {Dataset for de novo transcriptome assembly of the {African} bullfrog {Pyxicephalus} adspersus},
- url = {http://www.sciencedirect.com/science/article/pii/S2352340920302821},
- urldate = {2020-03-23},
- volume = {30},
- year = {2020}
-}
-
-@article{youssar_intercellular_2019,
- abstract = {Nematode-trapping fungi (NTF) are a large and diverse group of fungi, which may switch from a saprotrophic to a predatory livestyle if nematodes are present. Different fungi have developed different trapping devices, ranging from adhesive cells to constricting rings. After trapping, fungal hyphae penetrate the worm, secrete lytic enzymes and form a hyphal network inside the body. We sequenced the genome of Duddingtonia flagrans, a biotechnologically important NTF used to control nematode populations in fields. The 36.64 Mb genome encodes 9,927 putative proteins, among which are more than 638 predicted secreted proteins. Most secreted proteins are lytic enzymes, but more than 200 were classified as small secreted proteins ({\textless} 300 amino acids). 117 putative effector proteins were predicted, suggesting interkingdom communication during the colonization. As a first step to analyze the function of such proteins or other phenomena at the molecular level, we developed a transformation system, established the fluorescent proteins GFP and mCherry, adapted an assay to monitor protein secretion, and established gene-deletion protocols using homologous recombination or CRISPR/Cas9. One putative effector protein, PefB, was transcriptionally induced during the interaction. We show that the mature protein is able to be imported into nuclei in C. elegans cells. In addition, we studied trap formation and show that cell-to-cell communication is required for ring closure. The availability of the genome sequence and the establishment of many molecular tools will open new avenues to studying this biotechnologically relevant nematode-trapping fungus.},
- author = {Youssar, Loubna and Wernet, Valentin and Hensel, Nicole and Yu, Xi and Hildebrand, Heinz-Georg and Schreckenberger, Birgit and Kriegler, Marius and Hetzer, Birgit and Frankino, Phillip and Dillin, Andrew and Fischer, Reinhard},
- doi = {10.1371/journal.pgen.1008029},
- issn = {1553-7404},
- journal = {PLOS Genetics},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Fungal genetics, Fungal genomics, Fungi, Nematode infections, Protein domains, Proteomes, RNA extraction},
- language = {en},
- month = {March},
- number = {3},
- pages = {e1008029},
- title = {Intercellular communication is required for trap formation in the nematode-trapping fungus {Duddingtonia} flagrans},
- url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008029},
- urldate = {2019-04-06},
- volume = {15},
- year = {2019}
-}
-
-@article{yu_bromodomain-containing_2021,
- abstract = {Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machines that play vital roles in the regulation of chromatin structure and gene expression. However, the mechanisms by which SWI/SNF complexes recognize their target loci in plants are not fully understood. Here, we show that the Arabidopsis thaliana bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and critical for SWI/SNF genomic targeting. These three BRDs interact directly with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit. Phenotypic and transcriptomic analyses of the brd1 brd2 brd13 triple mutant revealed that these BRDs act largely redundantly to control gene expression and developmental processes that are also regulated by BRM. Genome-wide occupancy profiling demonstrated that these three BRDs extensively colocalize with BRM on chromatin. Simultaneous loss of function of three BRD genes results in reduced BRM protein levels and decreased occupancy of BRM on chromatin across the genome. Furthermore, we demonstrated that the bromodomains of BRDs are essential for genomic targeting of the BRD subunits of SWI/SNF complexes to their target sites. Collectively, these results demonstrate that BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and reveal their biological roles in facilitating genomic targeting of BRM-containing SWI/SNF complexes in plants.},
- author = {Yu, Yaoguang and Fu, Wei and Xu, Jianqu and Lei, Yawen and Song, Xin and Liang, Zhenwei and Zhu, Tao and Liang, Yuhui and Hao, Yuanhao and Yuan, Liangbing and Li, Chenlong},
- doi = {10.1016/j.molp.2021.03.018},
- issn = {1674-2052},
- journal = {Molecular Plant},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, BRAHMA, SWI/SNF complexes, bromodomain, chromatin remodeling},
- language = {en},
- month = {June},
- number = {6},
- pages = {888--904},
- title = {Bromodomain-containing proteins {BRD1}, {BRD2}, and {BRD13} are core subunits of {SWI}/{SNF} complexes and vital for their genomic targeting in {Arabidopsis}},
- url = {https://www.sciencedirect.com/science/article/pii/S1674205221000939},
- urldate = {2021-07-21},
- volume = {14},
- year = {2021}
-}
-
-@article{zavala-alvarado_transcriptional_2020,
- abstract = {Pathogenic Leptospira spp. are the causative agents of the waterborne zoonotic disease leptospirosis. Leptospira are challenged by numerous adverse conditions, including deadly reactive oxygen species (ROS), when infecting their hosts. Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. In L. interrogans, genes encoding defenses against ROS are repressed by the peroxide stress regulator, PerR. In this study, RNA sequencing was performed to characterize both the L. interrogans response to low and high concentrations of hydrogen peroxide and the PerR regulon. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to detoxify oxidants produced during peroxide stress. In addition, canonical molecular chaperones of the heat shock response and DNA repair proteins from the SOS response were required for Leptospira recovering from oxidative damage. Identification of the PerR regulon upon exposure to H2O2 allowed to define the contribution of this regulator in the oxidative stress response. This study has revealed a PerR-independent regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, the oxidative stress response. We have shown that PerR-regulated genes encoding a TonB-dependent transporter and a two-component system (VicKR) are involved in Leptospira tolerance to superoxide. This could represent the first defense mechanism against superoxide in L. interrogans, a bacterium lacking canonical superoxide dismutase. Our findings provide an insight into the mechanisms required by pathogenic Leptospira to overcome oxidative damage during infection-related conditions. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms in this life-threatening pathogen.},
- author = {Zavala-Alvarado, Crispin and Sismeiro, Odile and Legendre, Rachel and Varet, Hugo and Bussotti, Giovanni and Bayram, Jan and Huete, Samuel G. and Rey, Guillaume and Coppée, Jean-Yves and Picardeau, Mathieu and Benaroudj, Nadia},
- doi = {10.1371/journal.ppat.1008904},
- issn = {1553-7374},
- journal = {PLOS Pathogens},
- keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Bacterial pathogens, Gene expression, Gene prediction, Hydrogen peroxide, Leptospira, Leptospira interrogans, Non-coding RNA, Operons},
- language = {en},
- month = {October},
- note = {Publisher: Public Library of Science},
- number = {10},
- pages = {e1008904},
- title = {The transcriptional response of pathogenic {Leptospira} to peroxide reveals new defenses against infection-related oxidative stress},
- url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008904},
- urldate = {2021-05-15},
- volume = {16},
- year = {2020}
-}
-
-@article{zhuang_time-_2021,
- author = {Zhuang, Xinyu and Schlunck, Günther and Wolf, Julian and Rosmus, Dennis-Dominik and Bleul, Tim and Luo, Ren and Böhringer, Daniel and Wieghofer, Peter and Lange, Clemens and Reinhard, Thomas and Lapp, Thabo},
- doi = {10.1159/000516669},
- keywords = {+UsePublic, {\textgreater}UseGalaxy.eu},
- month = {June},
- note = {Publisher: S. Karger AG},
- pages = {1--14},
- title = {Time- and {Stimulus}-{Dependent} {Characteristics} of {Innate} {Immune} {Cells} in {Organ}-{Cultured} {Human} {Corneal} {Tissue}},
- url = {https://doi.org/10.1159/000516669},
- year = {2021}
-}
-