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| 1 | +- title: "Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer" |
| 2 | + authors: Jared T Simpson, Rachael Workman, Philip C Zuzarte, Matei David, Lewis Jonathan Dursi, Winston Timp |
| 3 | + year: 2017 |
| 4 | + preprint: 0 |
| 5 | + link: |
| 6 | + url: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4184.html |
| 7 | + display: "Nature Methods" |
| 8 | + |
| 9 | +- title: "Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas" |
| 10 | + authors: Nuno R Faria, Josh Quick, Ingra Morales, Julien Theze, Jacqueline G de Jesus, Marta Giovanetti, Moritz UG Kraemer, Sarah C Hill et al. |
| 11 | + year: 2017 |
| 12 | + preprint: 1 |
| 13 | + link: |
| 14 | + url: http://biorxiv.org/content/early/2017/02/02/105171 |
| 15 | + display: "bioRxiv" |
| 16 | + |
| 17 | +- title: "De novo genome and transcriptome assembly of the Canadian beaver (Castor canadensis)" |
| 18 | + authors: Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan KC Yuen, Wilson WL Sung, Joseph Whitney et al. |
| 19 | + year: 2017 |
| 20 | + preprint: 0 |
| 21 | + link: |
| 22 | + url: http://www.g3journal.org/content/early/2017/01/13/g3.116.038208.1 |
| 23 | + display: "G3: Genes, Genomes, Genetics" |
| 24 | + |
| 25 | +- title: "Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples" |
| 26 | + authors: Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka et al. |
| 27 | + year: 2017 |
| 28 | + preprint: 1 |
| 29 | + link: |
| 30 | + url: http://biorxiv.org/content/early/2017/01/09/098913 |
| 31 | + display: "bioRxiv" |
| 32 | + |
| 33 | +- title: "A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns" |
| 34 | + authors: Faiyaz Notta, Michelle Chan-Seng-Yue, Mathieu Lemire, Yilong Li, Gavin W Wilson, Ashton A Connor, Robert E Denroche, Sheng-Ben Liang et al. |
| 35 | + year: 2016 |
| 36 | + preprint: 0 |
| 37 | + link: |
| 38 | + url: http://www.nature.com/nature/journal/v538/n7625/full/nature19823.html |
| 39 | + display: "Nature" |
| 40 | + |
| 41 | +- title: "Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly" |
| 42 | + authors: Valerie A Schneider, Tina Graves Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt et al. |
| 43 | + year: 2016 |
| 44 | + preprint: 1 |
| 45 | + link: |
| 46 | + url: http://biorxiv.org/content/early/2016/08/30/072116 |
| 47 | + display: "bioRxiv" |
| 48 | + |
| 49 | +- title: "Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes" |
| 50 | + authors: Dirk-Dominic Dolle, Zhicheng Liu, Matthew L Cotten, Jared T Simpson, Zamin Iqbal, Richard Durbin, Shane A McCarthy, Thomas M Keane |
| 51 | + year: 2016 |
| 52 | + preprint: 0 |
| 53 | + link: |
| 54 | + url: http://genome.cshlp.org/content/27/2/300.abstract |
| 55 | + display: "Genome Research" |
| 56 | + |
| 57 | +- title: "A global reference for human genetic variation" |
| 58 | + authors: 1000 Genomes Project Consortium et al. |
| 59 | + year: 2015 |
| 60 | + preprint: 0 |
| 61 | + link: |
| 62 | + url: http://www.nature.com/nature/journal/v526/n7571/full/nature15393.html |
| 63 | + display: "Nature" |
| 64 | + |
| 65 | +- title: "trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios" |
| 66 | + authors: Milan Malinsky, Jared T Simpson, Richard Durbin |
| 67 | + year: 2016 |
| 68 | + preprint: 1 |
| 69 | + link: |
| 70 | + url: http://biorxiv.org/content/early/2016/05/03/051516 |
| 71 | + display: "bioRxiv" |
| 72 | + |
| 73 | +- title: "Nanocall: an open source basecaller for Oxford Nanopore sequencing data" |
| 74 | + authors: Matei David, Lewis Jonathan Dursi, Delia Yao, Paul C Boutros, Jared T Simpson |
| 75 | + year: 2016 |
| 76 | + preprint: 0 |
| 77 | + link: |
| 78 | + url: https://academic.oup.com/bioinformatics/article/33/1/49/2525680/Nanocall-an-open-source-basecaller-for-Oxford |
| 79 | + display: "Bioinformatics" |
| 80 | + |
| 81 | +- title: "Real-time, portable genome sequencing for Ebola surveillance" |
| 82 | + authors: Joshua Quick, Nicholas J Loman, Sophie Duraffour, Jared T Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno et al. |
| 83 | + year: 2016 |
| 84 | + preprint: 0 |
| 85 | + link: |
| 86 | + url: http://www.nature.com/nature/journal/v530/n7589/full/nature16996.html |
| 87 | + display: "Nature" |
| 88 | + |
| 89 | +- title: "A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing" |
| 90 | + authors: Tyler S Alioto, Ivo Buchhalter, Sophia Derdak, Barbara Hutter, Matthew D Eldridge, Eivind Hovig, Lawrence E Heisler, Timothy A Beck et al. |
| 91 | + year: 2015 |
| 92 | + preprint: 0 |
| 93 | + link: |
| 94 | + url: http://www.nature.com/articles/ncomms10001 |
| 95 | + display: "Nature communications" |
| 96 | + |
| 97 | +- title: "MinION Analysis and Reference Consortium: Phase 1 data release and analysis" |
| 98 | + authors: Camilla LC Ip, Matthew Loose, John R Tyson, Mariateresa de Cesare, Bonnie L Brown, Miten Jain, Richard M Leggett, David A Eccles et al. |
| 99 | + year: 2015 |
| 100 | + preprint: 0 |
| 101 | + link: |
| 102 | + url: https://f1000research.com/articles/4-1075/v1 |
| 103 | + display: "F1000Research" |
| 104 | + |
| 105 | +- title: "The khmer software package: enabling efficient nucleotide sequence analysis" |
| 106 | + authors: Michael R Crusoe, Hussien F Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides et al. |
| 107 | + year: 2015 |
| 108 | + preprint: 0 |
| 109 | + link: |
| 110 | + url: https://f1000research.com/articles/4-900/v1 |
| 111 | + display: "F1000Research" |
| 112 | + |
| 113 | +- title: "A complete bacterial genome assembled de novo using only nanopore sequencing data" |
| 114 | + authors: Nicholas J Loman, Joshua Quick, Jared T Simpson |
| 115 | + year: 2015 |
| 116 | + preprint: 0 |
| 117 | + link: |
| 118 | + url: http://www.nature.com/nmeth/journal/v12/n8/full/nmeth.3444.html |
| 119 | + display: "Nature methods" |
| 120 | + |
| 121 | +- title: "The genomic and phenotypic diversity of Schizosaccharomyces pombe" |
| 122 | + authors: Daniel C Jeffares, Charalampos Rallis, Adrien Rieux, Doug Speed, Martin P{ř}evorovsk{ỳ}, Tobias Mourier, Francesc X Marsellach, Zamin Iqbal et al. |
| 123 | + year: 2015 |
| 124 | + preprint: 0 |
| 125 | + link: |
| 126 | + url: http://www.nature.com/ng/journal/v47/n3/full/ng.3215.html |
| 127 | + display: "Nature genetics" |
| 128 | + |
| 129 | +- title: "The theory and practice of genome sequence assembly" |
| 130 | + authors: Jared T Simpson, Mihai Pop |
| 131 | + year: 2015 |
| 132 | + preprint: 0 |
| 133 | + link: |
| 134 | + url: http://www.annualreviews.org/doi/abs/10.1146/annurev-genom-090314-050032?journalCode=genom |
| 135 | + display: "Annual review of genomics and human genetics" |
| 136 | + |
| 137 | +- title: "A high-definition view of functional genetic variation from natural yeast genomes" |
| 138 | + authors: Anders Bergström, Jared T Simpson, Francisco Salinas, Benjamin Barré, Leopold Parts, Amin Zia, Alex N Nguyen Ba, Alan M Moses et al. |
| 139 | + year: 2014 |
| 140 | + preprint: 0 |
| 141 | + link: |
| 142 | + url: https://academic.oup.com/mbe/article/31/4/872/1103434/A-High-Definition-View-of-Functional-Genetic |
| 143 | + display: "Molecular biology and evolution" |
| 144 | + |
| 145 | +- title: "Exploring genome characteristics and sequence quality without a reference" |
| 146 | + authors: Jared T Simpson |
| 147 | + year: 2014 |
| 148 | + preprint: 0 |
| 149 | + link: |
| 150 | + url: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu023 |
| 151 | + display: "Bioinformatics" |
| 152 | + |
| 153 | +- title: "Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species" |
| 154 | + authors: Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inan{ç} Birol, Sébastien Boisvert, Jarrod A Chapman et al. |
| 155 | + year: 2013 |
| 156 | + preprint: 0 |
| 157 | + link: |
| 158 | + url: https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-2-10 |
| 159 | + display: "GigaScience" |
| 160 | + |
| 161 | +- title: "Insights into hominid evolution from the gorilla genome sequence" |
| 162 | + authors: Aylwyn Scally, Julien Y Dutheil, LaDeana W Hillier, Gregory E Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen et al. |
| 163 | + year: 2012 |
| 164 | + preprint: 0 |
| 165 | + link: |
| 166 | + url: http://www.nature.com/nature/journal/v483/n7388/full/nature10842.html |
| 167 | + display: "Nature" |
| 168 | + |
| 169 | +- title: "Efficient de novo assembly of large genomes using compressed data structures" |
| 170 | + authors: Jared T Simpson, Richard Durbin |
| 171 | + year: 2012 |
| 172 | + preprint: 0 |
| 173 | + link: |
| 174 | + url: http://genome.cshlp.org/content/early/2011/12/07/gr.126953.111 |
| 175 | + display: "Genome research" |
| 176 | + |
| 177 | +- title: "Assemblathon 1: a competitive assessment of de novo short read assembly methods" |
| 178 | + authors: Dent Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo et al. |
| 179 | + year: 2011 |
| 180 | + preprint: 0 |
| 181 | + link: |
| 182 | + url: http://genome.cshlp.org/content/early/2011/09/16/gr.126599.111.abstract |
| 183 | + display: "Genome research" |
| 184 | + |
| 185 | +- title: "Trait variation in yeast is defined by population history" |
| 186 | + authors: Jonas Warringer, Enikö Zörgö, Francisco A Cubillos, Amin Zia, Arne Gjuvsland, Jared T Simpson, Annabelle Forsmark, Richard Durbin et al. |
| 187 | + year: 2011 |
| 188 | + preprint: 0 |
| 189 | + link: |
| 190 | + url: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002111 |
| 191 | + display: "PLoS Genet" |
| 192 | + |
| 193 | +- title: "Copy number variant detection in inbred strains from short read sequence data" |
| 194 | + authors: Jared T Simpson, Rebecca E McIntyre, David J Adams, Richard Durbin |
| 195 | + year: 2010 |
| 196 | + preprint: 0 |
| 197 | + link: |
| 198 | + url: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp693 |
| 199 | + display: "Bioinformatics" |
| 200 | + |
| 201 | +- title: "Revealing the genetic structure of a trait by sequencing a population under selection" |
| 202 | + authors: Leopold Parts, Francisco A Cubillos, Jonas Warringer, Kanika Jain, Francisco Salinas, Suzannah J Bumpstead, Mikael Molin, Amin Zia et al. |
| 203 | + year: 2011 |
| 204 | + preprint: 0 |
| 205 | + link: |
| 206 | + url: http://genome.cshlp.org/content/21/7/1131.full |
| 207 | + display: "Genome research" |
| 208 | + |
| 209 | +- title: "Efficient construction of an assembly string graph using the FM-index" |
| 210 | + authors: Jared T Simpson, Richard Durbin |
| 211 | + year: 2010 |
| 212 | + preprint: 0 |
| 213 | + link: |
| 214 | + url: https://academic.oup.com/bioinformatics/article/26/12/i367/286190/Efficient-construction-of-an-assembly-string-graph |
| 215 | + display: "Bioinformatics" |
| 216 | + |
| 217 | +- title: "Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels" |
| 218 | + authors: Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch et al. |
| 219 | + year: 2009 |
| 220 | + preprint: 0 |
| 221 | + link: |
| 222 | + url: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-10-r112 |
| 223 | + display: "Genome biology" |
| 224 | + |
| 225 | +- title: "Complex landscapes of somatic rearrangement in human breast cancer genomes" |
| 226 | + authors: Philip J Stephens, David J McBride, Meng-Lay Lin, Ignacio Varela, Erin D Pleasance, Jared T Simpson, Lucy A Stebbings, Catherine Leroy et al. |
| 227 | + year: 2009 |
| 228 | + preprint: 0 |
| 229 | + link: |
| 230 | + url: http://www.nature.com/nature/journal/v462/n7276/full/nature08645.html |
| 231 | + display: "Nature" |
| 232 | + |
| 233 | +- title: "ABySS: a parallel assembler for short read sequence data" |
| 234 | + authors: Jared T Simpson, Kim Wong, Shaun D Jackman, Jacqueline E Schein, Steven JM Jones, Inan{ç} Birol |
| 235 | + year: 2009 |
| 236 | + preprint: 0 |
| 237 | + link: |
| 238 | + url: http://genome.cshlp.org/content/19/6/1117 |
| 239 | + display: "Genome research" |
| 240 | + |
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