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All_refs.bib
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%% Created using Papers on Mon, 12 Oct 2015.
%% http://papersapp.com/papers/
@article{Alberts:2005je,
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year = {2005},
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month = nov
}
@article{Milani:2009ua,
author = {Milani, Lili and Lundmark, Anders and Nordlund, Jessica and Kiialainen, Anna and Flaegstad, Trond and Jonmundsson, Gudmundur and Kanerva, Jukka and Schmiegelow, Kjeld and Gunderson, Kevin and L nnerholm, Gudmar and Syv nen, Ann-Christine},
title = {{Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation}},
journal = {Genome Res},
year = {2009},
volume = {19},
number = {1},
pages = {1--11},
annote = {10.1101/gr.083931.108}
}
@article{Mercer:2009vz,
author = {Mercer, Tim and Dinger, Marcel and Mattick, John},
title = {{Long non-coding RNAs: insights into functions}},
journal = {Nat Rev Genet},
year = {2009},
volume = {10},
number = {3},
pages = {155--159},
annote = {10.1038/nrg2521}
}
@article{Lynch:2009gv,
author = {Lynch, Andy and Dunning, MJ and Iddawela, M and Barbosa-Morais, Nuno and Ritchie, ME},
title = {{Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms}},
journal = {Statistical Methods in Medical Research},
year = {2009},
pages = {0962280208099451}
}
@article{Lenser:2009vj,
author = {Lenser, Thorsten and Thei {\"u}en, G {\textordmasculine}nter and Dittrich, Peter},
title = {{Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins}},
journal = {PLoS Comput Biol},
year = {2009},
volume = {5},
number = {1},
pages = {e1000264}
}
@article{FalloutRubio:2009tc,
author = {Fallout-Rubio, D and Guibal, F and Klein, E and M, Bariteaum and Lefevre, F},
title = {{Rapid changes in plasticity across generations within an expanding cedar forest}},
journal = {J Evol Biol},
year = {2009},
volume = {22},
number = {3},
pages = {553--563},
annote = {10.1111/j.1420-9101.2008.01662.x}
}
@article{Zucchetti:2008he,
author = {Zucchetti, I and Marino, R and Pinto, M and Lambris, J and Du Pasquier, L and De Santis, R},
title = {{ciCD94-1, an ascidian multipurpose C-type lectin-like receptor expressed in Ciona intestinalis hemocytes and larval neural structures}},
journal = {Differentiation},
year = {2008},
volume = {76},
number = {3},
pages = {267--282},
month = mar,
annote = {Zucchetti, IvanaMarino, RitaPinto, Maria RosariaLambris, John DDu Pasquier, LouisDe Santis, RosariaEnglandDifferentiation; research in biological diversityDifferentiation. 2008 Mar;76(3):267-82. Epub 2007 Oct 9.}
}
@article{Zhu:2008ec,
author = {Zhu, J and Zhang, B and Smith, E and Drees, B and Brem, R and Kruglyak, L and Bumgarner, R and Schadt, E},
title = {{Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks}},
journal = {Nat Genet},
year = {2008},
volume = {40},
number = {7},
pages = {854--861},
month = jul,
annote = {Zhu, JunZhang, BinSmith, Erin NDrees, BeckyBrem, Rachel BKruglyak, LeonidBumgarner, Roger ESchadt, Eric EP50GM071508/GM/United States NIGMSR37 MH059520/MH/United States NIMHResearch Support, N.I.H., ExtramuralValidation StudiesUnited StatesNature geneticsNat Genet. 2008 Jul;40(7):854-61. Epub 2008 Jun 15.}
}
@article{Zabel:2008ct,
author = {Zabel, C and Mao, L and Woodman, B and Rohe, M and Wacker, M and Klaere, Y and Koppelstaetter, A and Nebrich, G and Klein, O and Grams, S and Strand, A and Luthi-Carter, R and Hartl, Daniel L and Klose, J and Bates, G},
title = {{A large number of protein expression changes occur early in life and precede phenotype onset in a mouse model for Huntington's disease}},
journal = {Mol Cell Proteomics},
year = {2008},
month = dec,
annote = {Journal articleMolecular {\&}amp; cellular proteomics : MCPMol Cell Proteomics. 2008 Dec 8.}
}
@article{Zabel:2008dr,
author = {Zabel, C and Andreew, A and Mao, L and Hartl, Daniel L},
title = {{Protein expression overlap: more important than which proteins change in expression?}},
journal = {Expert Rev Proteomics},
year = {2008},
volume = {5},
number = {2},
pages = {187--205},
month = apr,
annote = {Zabel, ClausAndreew, AlexanderMao, LeiHartl, DanielaReviewEnglandExpert review of proteomicsExpert Rev Proteomics. 2008 Apr;5(2):187-205.}
}
@article{Yoshihara:2008kl,
author = {Yoshihara, M and Ueki, T and Yamaguchi, N and Kamino, K and Michibata, H},
title = {{Characterization of a novel vanadium-binding protein (VBP-129) from blood plasma of the vanadium-rich ascidian Ascidia sydneiensis samea}},
journal = {Biochim Biophys Acta},
year = {2008},
volume = {1780},
number = {2},
pages = {256--263},
month = feb,
annote = {Yoshihara, MasaoUeki, TatsuyaYamaguchi, NobuoKamino, KeiMichibata, HitoshiResearch Support, Non-U.S. Gov'tNetherlandsBiochimica et biophysica actaBiochim Biophys Acta. 2008 Feb;1780(2):256-63. Epub 2007 Nov 12.}
}
@article{Yagi:2008hu,
author = {Yagi, H and Nakagawa, M and Takahashi, N and Kondo, S and Matsubara, M and Kato, K},
title = {{Neural complex-specific expression of xylosyl N-glycan in Ciona intestinalis}},
journal = {Glycobiology},
year = {2008},
volume = {18},
number = {2},
pages = {145--151},
month = feb,
annote = {Yagi, HirokazuNakagawa, MasashiTakahashi, NorikoKondo, SachikoMatsubara, MamoruKato, KoichiResearch Support, Non-U.S. Gov'tEnglandGlycobiologyGlycobiology. 2008 Feb;18(2):145-51. Epub 2007 Dec 3.}
}
@article{Wong:2008us,
author = {Wong, WC and Loh, M and Eisenhaber, F},
title = {{On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation}},
journal = {Biology Direct},
year = {2008},
volume = {3},
pages = {23}
}
@article{Wittkopp:2008wr,
author = {Wittkopp, Patricia and Haerum, Belinda and Clark, Andrew},
title = {{Regulatory changes underlying expression differences within and between Drosophila species}},
journal = {Nat Genet},
year = {2008},
volume = {40},
number = {3},
pages = {346--350},
annote = {10.1038/ng.77}
}
@article{Wittkopp:2008ge,
author = {Wittkopp, Patricia and Haerum, Belinda and Clark, Andrew},
title = {{Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster}},
journal = {Genetics},
year = {2008},
pages = {genetics.107.082032},
month = feb
}
@article{Wang:2008wa,
author = {Wang, Eric and Sandberg, Rickard and Luo, Shujun and Khrebtukova, Irina and Zhang, Lu and Mayr, Christine and Kingsmore, Stephen and Schroth, Gary and Burge, Christopher},
title = {{Alternative isoform regulation in human tissue transcriptomes}},
journal = {Nature},
year = {2008},
annote = {10.1038/nature07509}
}
@article{Walters:2008tz,
author = {Walters, Jenna and Binkley, Elaine and Haygood, Ralph and Romano, Laura},
title = {{Evolutionary analysis of the cis-regulatory region of the spicule matrix gene SM50 in strongylocentrotid sea urchins}},
journal = {Developmental Biology},
year = {2008},
volume = {315},
number = {2},
pages = {567--578}
}
@article{Walter:2008ct,
author = {Walter, H and Schlaff, W and Lesch, O and Vitek, L and Zima, T and Hartl, Daniel L and Dvorak, A and Gutierrez-Lobos, K and Thau, K and De Witte, P},
title = {{Breath alcohol level and plasma amino acids: a comparison between older and younger chronic alcohol-dependent patients}},
journal = {Alcohol Alcohol},
year = {2008},
volume = {43},
number = {6},
pages = {653--657},
month = nov,
annote = {Walter, HenrietteSchlaff, William BLesch, Otto MVitek, LiborZima, TomasHartl, DorisDvorak, AlexanderGutierrez-Lobos, KarinThau, KennethDe Witte, PhilippeEnglandAlcohol and alcoholism (Oxford, Oxfordshire)Alcohol Alcohol. 2008 Nov-Dec;43(6):653-7. Epub 2008 Sep 22.}
}
@book{Walsh:2008wp,
author = {Walsh, Adrian and Lynch, Tony},
title = {{The morality of money : an exploration in analytic philosophy}},
year = {2008},
annote = {2008016328Adrian Walsh and Tony Lynch.Includes bibliographical references and index.}
}
@article{Vizzini:2008fu,
author = {Vizzini, A and Pergolizzi, M and Vazzana, M and Salerno, G and Di Sano, C and Macaluso, P and Arizza, V and Parrinello, D and Cammarata, M and Parrinello, N},
title = {{FACIT collagen (1alpha-chain) is expressed by hemocytes and epidermis during the inflammatory response of the ascidian Ciona intestinalis}},
journal = {CURR TOP DEV BIOL},
year = {2008},
volume = {32},
number = {6},
pages = {682--692},
annote = {Vizzini, AitiPergolizzi, MargheritaVazzana, MirellaSalerno, GiuseppinaDi Sano, CaterinaMacaluso, PasqualeArizza, VincenzoParrinello, DanielaCammarata, MatteoParrinello, NicoloResearch Support, Non-U.S. Gov'tUnited StatesDevelopmental and comparative immunologyDev Comp Immunol. 2008;32(6):682-92. Epub 2007 Nov 9.}
}
@article{Veyrieras:2008ts,
author = {Veyrieras, J and Kudaravalli, S and Kim, S and Dermitzakis, E and Gilad, Y and Stephens, M and Pritchard, Jonathan K},
title = {{High-resolution mapping of expression-QTLs yields insight into human gene regulation}},
journal = {PLoS Genet},
year = {2008},
volume = {4},
number = {10},
pages = {e1000214},
month = oct,
annote = {GM077959/GM/United States NIGMSHG002772/HG/United States NHGRIHG02585-01/HG/United States NHGRIUnited States Howard Hughes Medical InstituteJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tUnited States}
}
@article{Veeman:2008hj,
author = {Veeman, M and Nakatani, Y and Hendrickson, C and Ericson, V and Lin, C and Smith, W},
title = {{Chongmague reveals an essential role for laminin-mediated boundary formation in chordate convergence and extension movements}},
journal = {Development},
year = {2008},
volume = {135},
number = {1},
pages = {33--41},
annote = {Veeman, Michael TNakatani, YukiHendrickson, CarolynEricson, VivianLin, ClarissaSmith, William CGM075049/GM/United States NIGMSHD038701/HD/United States NICHDResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tEnglandDevelopment (Cambridge, England)Development. 2008 Jan;135(1):33-41. Epub 2007 Nov 21.}
}
@article{Terasaki:2008cf,
author = {Terasaki, A and Hiruta, J and Suzuki, J and Sakamoto, S and Nishioka, T and Suzuki, H and Ohashi, K and Azumi, K and Ogasawara, M},
title = {{A lasp family protein of Ciona intestinalis}},
journal = {Biochim Biophys Acta},
year = {2008},
volume = {1779},
number = {1},
pages = {51--59},
annote = {Terasaki, Asako GHiruta, JinSuzuki, JunkoSakamoto, SachikoNishioka, TatsujiSuzuki, HiroshiOhashi, KazuyoAzumi, KaoruOgasawara, MichioResearch Support, Non-U.S. Gov'tNetherlandsBiochimica et biophysica actaBiochim Biophys Acta. 2008 Jan;1779(1):51-9. Epub 2007 Dec 3.}
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@article{Stylianou:2008hn,
author = {Stylianou, Ioannis and Affourtit, Jason and Shockley, Keith and Wilpan, Rob and Abdi, Fadi and Bhardwaj, Sanjeev and Rollins, Jarod and Churchill, Gary and Paigen, Beverly},
title = {{Applying Gene Expression, Proteomics and SNP Analysis for Complex Trait Gene Identification}},
journal = {Genetics},
year = {2008},
pages = {genetics.107.081216},
month = feb
}
@article{Smith:2008th,
author = {Smith, Joel and Davidson, Eric},
title = {{Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {51},
pages = {20089--20094},
annote = {10.1073/pnas.0806442105}
}
@article{Smith:2008vy,
author = {Smith, E and Kruglyak, L},
title = {{Gene-environment interaction in yeast gene expression}},
journal = {PLoS Biol},
year = {2008},
volume = {6},
number = {4},
pages = {e83},
month = apr,
annote = {GM071508/GM/United States NIGMSP50 GM071508/GM/United States NIGMSR37 MH059520/MH/United States NIMHJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tUnited States}
}
@article{Schuchhardt:2008iz,
author = {Schuchhardt, Johannes and Glintschert, A and Hartl, Daniel L and Irmler, M and Beckers, J and Stephan, C and Marcus, K and Klose, J and Meyer, H and Malik, A},
title = {{BrainProfileDB - a platform for integration of functional genomics data}},
journal = {Proteomics},
year = {2008},
volume = {8},
number = {6},
pages = {1162--1164},
month = mar,
annote = {Schuchhardt, JohannesGlintschert, AlexanderHartl, DanielaIrmler, MartinBeckers, JohannesStephan, ChristianMarcus, KatrinKlose, JoachimMeyer, Helmut EMalik, ArifResearch Support, Non-U.S. Gov'tGermanyProteomicsProteomics. 2008 Mar;8(6):1162-4.}
}
@article{SchaefferSW:2008tw,
author = {Schaeffer SW, Bhutkar},
title = {{Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps}},
journal = {Genetics in press.},
year = {2008},
volume = {20 May 2008}
}
@article{Roy:2008eo,
author = {Roy, S and Ferreira, M and Hartl, Daniel L},
title = {{Evolution of allelic dimorphism in malarial surface antigens}},
journal = {Heredity},
year = {2008},
volume = {100},
number = {2},
pages = {103--110},
month = feb,
annote = {Roy, S WFerreira, M UHartl, D LResearch Support, Non-U.S. Gov'tReviewEnglandHeredityHeredity. 2008 Feb;100(2):103-10. Epub 2006 Oct 4.}
}
@article{Roux:2008ue,
author = {Roux, Julien and Robinson-Rechavi, Marc},
title = {{Developmental Constraints on Vertebrate Genome Evolution}},
journal = {PLoS Genet},
year = {2008},
volume = {4},
number = {12},
pages = {e1000311}
}
@article{Rottinger:2008vy,
author = {Rottinger, Eric and Saudemont, A and Duboc, V and Besnardeau, Lydia and McClay, D and Lepage, T},
title = {{FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis of the skeleton and regulate gastrulation during sea urchin development}},
journal = {Development},
year = {2008},
volume = {135},
number = {2},
pages = {353}
}
@article{Rogers:2008he,
author = {Rogers, R and Bedford, T and Hartl, Daniel L},
title = {{Formation and Longevity of Chimeric and Duplicate Genes in Drosophila melanogaster}},
journal = {Genetics},
year = {2008},
month = nov,
annote = {Journal articleGeneticsGenetics. 2008 Nov 17.}
}
@article{Rieber:2008jb,
author = {Rieber, N and Graf, A and Belohradsky, B and Hartl, Daniel L and Urschel, S and Riffelmann, M and Wirsing von Konig, C and Liese, J},
title = {{Differences of humoral and cellular immune response to an acellular pertussis booster in adolescents with a whole cell or acellular primary vaccination}},
journal = {Vaccine},
year = {2008},
volume = {26},
number = {52},
pages = {6929--6935},
month = dec,
annote = {Rieber, NikolausGraf, AnnaBelohradsky, Bernd HHartl, DominikUrschel, SimonRiffelmann, MarionWirsing von Konig, Carl-HeinzLiese, JohannesNetherlandsVaccineVaccine. 2008 Dec 9;26(52):6929-35. Epub 2008 Oct 11.}
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author = {Sewell, M and Byrne, M},
title = {{Fuels for development: evolution of maternal provisioning in asterinid sea stars}},
journal = {Marine Biology},
year = {2008},
volume = {153},
number = {3},
pages = {337--349}
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author = {Prodon, F and Sardet, C and Nishida, H},
title = {{Cortical and cytoplasmic flows driven by actin microfilaments polarize the cortical ER-mRNA domain along the a-v axis in ascidian oocytes}},
journal = {Developmental Biology},
year = {2008},
volume = {313},
number = {2},
pages = {682--699},
month = jan,
annote = {Prodon, FrancoisSardet, ChristianNishida, HirokiResearch Support, Non-U.S. Gov'tUnited StatesDevelopmental biologyDev Biol. 2008 Jan 15;313(2):682-99. Epub 2007 Nov 17.}
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author = {Pouilhes, A and Kouklovsky, C and Langlois, Y and Baltaze, J and Vispe, S and Annereau, J and Barret, J and Kruczynski, A and Bailly, C},
title = {{Synthesis and biological evaluation of bengacarboline derivatives}},
journal = {Bioorg Med Chem Lett},
year = {2008},
volume = {18},
number = {3},
pages = {1212--1216},
month = feb,
annote = {Pouilhes, AnnieKouklovsky, CyrilleLanglois, YvesBaltaze, Jean-PierreVispe, StephaneAnnereau, Jean-PhilippeBarret, Jean-MarcKruczynski, AnnaBailly, ChristianEnglandBioorganic {\&}amp; medicinal chemistry lettersBioorg Med Chem Lett. 2008 Feb 1;18(3):1212-6. Epub 2007 Dec 4.}
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author = {Peschel, C and Hartmann, J and Schmittel, A and Bokemeyer, C and Schneller, F and Keilholz, U and Buchheidt, D and Millan, S and Izquierdo, M and Hofheinz, R},
title = {{Phase II study of plitidepsin in pretreated patients with locally advanced or metastatic non-small cell lung cancer}},
journal = {Lung Cancer},
year = {2008},
volume = {60},
number = {3},
pages = {374--380},
month = jun,
annote = {Peschel, ChristianHartmann, Joerg TSchmittel, AlexanderBokemeyer, CarstenSchneller, FolkerKeilholz, UlrichBuchheidt, DieterMillan, SusanaIzquierdo, Miguel AngelHofheinz, Ralf-DieterClinical Trial, Phase IIMulticenter StudyIrelandLung cancer (Amsterdam, Netherlands)Lung Cancer. 2008 Jun;60(3):374-80. Epub 2007 Dec 3.}
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author = {Oliveri, Paola and Tu, Qiang and Davidson, Eric},
title = {{Global regulatory logic for specification of an embryonic cell lineage}},
journal = {Proc Natl Acad Sci USA},
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volume = {105},
number = {16},
pages = {5955--5962},
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title = {{A single-cell view on the ecophysiology of anaerobic phototrophic bacteria}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {46},
pages = {17861--17866},
annote = {10.1073/pnas.0809329105}
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author = {Mao, L and Hartl, Daniel L and Nolden, T and Koppelstatter, A and Klose, J and Himmelbauer, H and Zabel, C},
title = {{Pronounced alterations of cellular metabolism and structure due to hyper- or hypo-osmosis}},
journal = {J Proteome Res},
year = {2008},
volume = {7},
number = {9},
pages = {3968--3983},
month = sep,
annote = {Mao, LeiHartl, DanielaNolden, TobiasKoppelstatter, AndreaKlose, JoachimHimmelbauer, HeinzZabel, ClausResearch Support, Non-U.S. Gov'tUnited StatesJournal of proteome researchJ Proteome Res. 2008 Sep;7(9):3968-83. Epub 2008 Jul 23.}
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author = {Lynch, M and Sung, W and Morris, K and Coffey, N and Landry, C and Dopman, E and Dickinson, W and Okamoto, K and Kulkarni, S and Hartl, Daniel L and Thomas, W},
title = {{A genome-wide view of the spectrum of spontaneous mutations in yeast}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {27},
pages = {9272--9277},
month = jul,
annote = {Lynch, MichaelSung, WayMorris, KrystalynneCoffey, NicoleLandry, Christian RDopman, Erik BDickinson, W JosephOkamoto, KazufusaKulkarni, ShilpaHartl, Daniel LThomas, W KelleyGM068465/GM/United States NIGMSGM36827/GM/United States NIGMSResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tUnited StatesProceedings of the National Academy of Sciences of the United States of AmericaProc Natl Acad Sci U S A. 2008 Jul 8;105(27):9272-7. Epub 2008 Jun 26.}
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author = {Luckenbach, T and Epel, D},
title = {{ABCB- and ABCC-type transporters confer multixenobiotic resistance and form an environment-tissue barrier in bivalve gills}},
journal = {Am J Physiol Regul Integr Comp Physiol},
year = {2008},
volume = {294},
number = {6},
pages = {R1919--29},
month = jun,
annote = {Luckenbach, TillEpel, DavidUnited StatesAmerican journal of physiology. Regulatory, integrative and comparative physiologyAm J Physiol Regul Integr Comp Physiol. 2008 Jun;294(6):R1919-29. Epub 2008 Apr 9.}
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author = {Luckenbach, T and Altenburger, R and Epel, D},
title = {{Teasing apart activities of different types of ABC efflux pumps in bivalve gills using the concepts of independent action and concentration addition}},
journal = {Mar Environ Res},
year = {2008},
volume = {66},
number = {1},
pages = {75--76},
month = jul,
annote = {Luckenbach, TillAltenburger, RolfEpel, DavidResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.EnglandMarine environmental researchMar Environ Res. 2008 Jul;66(1):75-6. Epub 2008 Feb 26.}
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author = {Lopez-Maury, L and Marguerat, S and Bahler, J},
title = {{Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation}},
journal = {Nat Rev Genet},
year = {2008},
volume = {9},
number = {8},
pages = {583--593},
month = aug,
annote = {Lopez-Maury, LuisMarguerat, SamuelBahler, JurgUnited Kingdom Cancer Research UKResearch Support, Non-U.S. Gov'tReviewEnglandNature reviews. GeneticsNat Rev Genet. 2008 Aug;9(8):583-93.}
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author = {Lofgren, S and Miletti, L and Steindel, M and Bachere, E and Barracco, M},
title = {{Trypanocidal and leishmanicidal activities of different antimicrobial peptides (AMPs) isolated from aquatic animals}},
journal = {Exp Parasitol},
year = {2008},
volume = {118},
number = {2},
pages = {197--202},
month = feb,
annote = {Lofgren, S EMiletti, L CSteindel, MBachere, EBarracco, M AResearch Support, Non-U.S. Gov'tUnited StatesExperimental parasitologyExp Parasitol. 2008 Feb;118(2):197-202. Epub 2007 Aug 15.}
}
@article{Liu:2008by,
author = {Liu, Bing and de la Fuente, Alberto and Hoeschele, Ina},
title = {{Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments}},
journal = {Genetics},
year = {2008},
pages = {genetics.107.080069},
month = feb
}
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author = {Lin, Simon and Du, Pan and Huber, Wolfgang and Kibbe, Warren},
title = {{Model-based variance-stabilizing transformation for Illumina microarray data}},
journal = {Nucl. Acids Res.},
year = {2008},
volume = {36},
number = {2},
month = feb
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@article{Liao:2008jz,
author = {Liao, X and Majithia, A and Huang, X and Kimmel, A},
title = {{Growth control via TOR kinase signaling, an intracellular sensor of amino acid and energy availability, with crosstalk potential to proline metabolism}},
journal = {Amino Acids},
year = {2008},
volume = {35},
number = {4},
pages = {761--770},
month = nov,
annote = {Liao, Xin-HuaMajithia, AmitHuang, XiuliKimmel, Alan RResearch Support, N.I.H., IntramuralAustriaAmino acidsAmino Acids. 2008 Nov;35(4):761-70. Epub 2008 Jul 24.}
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author = {Li, Y and Breitling, R and Jansen, R},
title = {{Generalizing genetical genomics: getting added value from environmental perturbation}},
journal = {Trends Genet},
year = {2008},
volume = {24},
number = {10},
pages = {518--524},
month = oct,
annote = {Li, YangBreitling, RainerJansen, Ritsert CEnglandTrends in genetics : TIGTrends Genet. 2008 Oct;24(10):518-24. Epub 2008 Sep 4.}
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@article{Lemos:2008jd,
author = {Lemos, B and Araripe, L and Hartl, Daniel L},
title = {{Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences}},
journal = {Science},
year = {2008},
volume = {319},
number = {5859},
pages = {91--93},
month = jan,
annote = {Lemos, BernardoAraripe, Luciana OHartl, Daniel LGM065169/GM/United States NIGMSGM068465/GM/United States NIGMSResearch Support, N.I.H., ExtramuralUnited StatesScience (New York, N.Y.)Science. 2008 Jan 4;319(5859):91-3.}
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@article{Lemos:2008br,
author = {Lemos, B and Araripe, L and Fontanillas, P and Hartl, Daniel L},
title = {{Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {38},
pages = {14471--14476},
month = sep,
annote = {Lemos, BernardoAraripe, Luciana OFontanillas, PierreHartl, Daniel LGM068465/GM/United States NIGMSResearch Support, N.I.H., ExtramuralUnited StatesProceedings of the National Academy of Sciences of the United States of AmericaProc Natl Acad Sci U S A. 2008 Sep 23;105(38):14471-6. Epub 2008 Sep 12.}
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author = {Lee, C and Hartl, Daniel L and Matsuura, H and Dunlop, F and Scotney, P and Fabri, L and Nash, A and Chen, N and Tang, C and Chen, Q and Homer, R and Baca, M and Elias, J},
title = {{Endogenous IL-11 signaling is essential in Th2- and IL-13-induced inflammation and mucus production}},
journal = {Am J Respir Cell Mol Biol},
year = {2008},
volume = {39},
number = {6},
pages = {739--746},
month = dec,
annote = {Lee, Chun GeunHartl, DominikMatsuura, HiroshiDunlop, Felicity MScotney, Pierre DFabri, Louis JNash, Andrew DChen, Ning-YuanTang, Chu-YanChen, QingshengHomer, Robert JBaca, ManuelElias, Jack AHL-084225/HL/United States NHLBIHL-56389/HL/United States NHLBIResearch Support, N.I.H., ExtramuralUnited StatesAmerican journal of respiratory cell and molecular biologyAm J Respir Cell Mol Biol. 2008 Dec;39(6):739-46. Epub 2008 Jul 10.}
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author = {Lee, C and Da Silva, C and Lee, J and Hartl, Daniel L and Elias, J},
title = {{Chitin regulation of immune responses: an old molecule with new roles}},
journal = {Curr Opin Immunol},
year = {2008},
volume = {20},
number = {6},
pages = {684--689},
month = dec,
annote = {Lee, Chun GeunDa Silva, Carla ALee, Jae-YoungHartl, DominikElias, Jack AEnglandCurrent opinion in immunologyCurr Opin Immunol. 2008 Dec;20(6):684-9. Epub 2008 Nov 1.}
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author = {Leboulleux, S and Dromain, C and Vataire, A and Malka, D and Auperin, A and Lumbroso, J and Duvillard, P and Elias, D and Hartl, Daniel L and De Baere, T and Guigay, J and Schlumberger, M and Ducreux, M and Baudin, E},
title = {{Prediction and diagnosis of bone metastases in well-differentiated gastro-entero-pancreatic endocrine cancer: a prospective comparison of whole body magnetic resonance imaging and somatostatin receptor scintigraphy}},
journal = {J Clin Endocrinol Metab},
year = {2008},
volume = {93},
number = {8},
pages = {3021--3028},
month = aug,
annote = {Leboulleux, SDromain, CVataire, A LMalka, DAuperin, ALumbroso, JDuvillard, PElias, DHartl, D MDe Baere, TGuigay, JSchlumberger, MDucreux, MBaudin, EComparative StudyUnited StatesThe Journal of clinical endocrinology and metabolismJ Clin Endocrinol Metab. 2008 Aug;93(8):3021-8. Epub 2008 Jun 3.}
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author = {Latzin, P and Hartl, Daniel L and Regamey, N and Frey, U and Schoeni, M and Casaulta, C},
title = {{Comparison of serum markers for allergic bronchopulmonary aspergillosis in cystic fibrosis}},
journal = {Eur Respir J},
year = {2008},
volume = {31},
number = {1},
pages = {36--42},
annote = {Latzin, PHartl, DRegamey, NFrey, USchoeni, M HCasaulta, CComparative StudyResearch Support, Non-U.S. Gov'tSwitzerlandThe European respiratory journal : official journal of the European Society for Clinical Respiratory PhysiologyEur Respir J. 2008 Jan;31(1):36-42. Epub 2007 Sep 26.}
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author = {Lahaye, R and van der Bank, M and Bogarin, D and Warner, J and Pupulin, F and Gigot, G and Maurin, O and Duthoit, S and Barraclough, T and Savolainen, V},
title = {{From the Cover: DNA barcoding the floras of biodiversity hotspots}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {8},
pages = {2923}
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author = {Kress, W and Erickson, D},
title = {{DNA barcodes: Genes, genomics, and bioinformatics}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {8},
pages = {2761}
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@article{KraussEtschmann:2008bb,
author = {Krauss-Etschmann, S and Hartl, Daniel L and Rzehak, P and Heinrich, J and Shadid, R and Del Carmen Ramirez-Tortosa, M and Campoy, C and Pardillo, S and Schendel, D and Decsi, T and Demmelmair, H and Koletzko, B},
title = {{Decreased cord blood IL-4, IL-13, and CCR4 and increased TGF-beta levels after fish oil supplementation of pregnant women}},
journal = {J Allergy Clin Immunol},
year = {2008},
volume = {121},
number = {2},
pages = {464--470 e6},
month = feb,
annote = {Krauss-Etschmann, SusanneHartl, DominikRzehak, PeterHeinrich, JoachimShadid, RaniaDel Carmen Ramirez-Tortosa, MariaCampoy, CristinaPardillo, SusanaSchendel, Dolores JDecsi, TamasDemmelmair, HansKoletzko, Berthold VNutraceuticals for Healthier Life Study GroupMulticenter StudyRandomized Controlled TrialResearch Support, Non-U.S. Gov'tUnited StatesThe Journal of allergy and clinical immunologyJ Allergy Clin Immunol. 2008 Feb;121(2):464-470.e6. Epub 2007 Nov 5.}
}
@article{Kormann:2008ct,
author = {Kormann, M and Depner, M and Hartl, Daniel L and Klopp, N and Illig, T and Adamski, J and Vogelberg, C and Weiland, S and von Mutius, E and Kabesch, M},
title = {{Toll-like receptor heterodimer variants protect from childhood asthma}},
journal = {J Allergy Clin Immunol},
year = {2008},
volume = {122},
number = {1},
pages = {86--92, 92 e1--8},
month = jul,
annote = {Kormann, Michael S DDepner, MartinHartl, DominikKlopp, NormanIllig, ThomasAdamski, JerzyVogelberg, ChristianWeiland, Stephan Kvon Mutius, ErikaKabesch, MichaelResearch Support, Non-U.S. Gov'tUnited StatesThe Journal of allergy and clinical immunologyJ Allergy Clin Immunol. 2008 Jul;122(1):86-92, 92.e1-8. Epub 2008 Jun 10.}
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author = {Koller, B and Kappler, M and Latzin, P and Gaggar, A and Schreiner, M and Takyar, S and Kormann, M and Kabesch, M and Roos, D and Griese, M and Hartl, Daniel L},
title = {{TLR expression on neutrophils at the pulmonary site of infection: TLR1/TLR2-mediated up-regulation of TLR5 expression in cystic fibrosis lung disease}},
journal = {J Immunol},
year = {2008},
volume = {181},
number = {4},
pages = {2753--2763},
month = aug,
annote = {Koller, BarbaraKappler, MatthiasLatzin, PhillipGaggar, AmitSchreiner, MarcusTakyar, SherkinKormann, MichaelKabesch, MichaelRoos, DirkGriese, MatthiasHartl, DominikComparative StudyResearch Support, Non-U.S. Gov'tUnited StatesJournal of immunology (Baltimore, Md. : 1950)J Immunol. 2008 Aug 15;181(4):2753-63.}
}
@article{Klingenberg:2008tf,
author = {Klingenberg, Christian Peter},
title = {{Morphological Integration and Developmental Modularity}},
journal = {Annu. Rev. Ecol. Evol. Syst},
year = {2008},
volume = {39},
pages = {115--132}
}
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author = {Kim, Minsung and Cui, Min-Long and Cubas, Pilar and Gillies, Amanda and Lee, Karen and Chapman, Mark and Abbott, Richard and Coen, Enrico},
title = {{Regulatory Genes Control a Key Morphological and Ecological Trait Transferred Between Species}},
journal = {Science},
year = {2008},
volume = {322},
number = {5904},
pages = {1116--1119},
month = nov
}
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author = {Kelley, Ryan and Feizi, Hoda and Ideker, Trey},
title = {{Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood}},
journal = {Bioinformatics},
year = {2008},
volume = {24},
number = {1},
pages = {71--77}
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author = {Kawamura, K and Sugino, Y and Sunanaga, T and Fujiwara, S},
title = {{Multipotent epithelial cells in the process of regeneration and asexual reproduction in colonial tunicates}},
journal = {Dev Growth Differ},
year = {2008},
volume = {50},
number = {1},
pages = {1--11},
annote = {Kawamura, KazuoSugino, YasuoSunanaga, TakeshiFujiwara, ShigekiResearch Support, Non-U.S. Gov'tReviewJapanDevelopment, growth {\&}amp; differentiationDev Growth Differ. 2008 Jan;50(1):1-11. Epub 2007 Nov 6.}
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author = {Karunaweera, N and Ferreira, M and Munasinghe, A and Barnwell, J and Collins, W and King, C and Kawamoto, F and Hartl, Daniel L and Wirth, D},
title = {{Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax}},
journal = {Gene},
year = {2008},
volume = {410},
number = {1},
pages = {105--112},
month = feb,
annote = {Karunaweera, Nadira DFerreira, Marcelo UMunasinghe, AnushaBarnwell, John WCollins, William EKing, Christopher LKawamoto, FumihikoHartl, Daniel LWirth, Dyann FR01 GM 061351/GM/United States NIGMSResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.NetherlandsGeneGene. 2008 Feb 29;410(1):105-12. Epub 2008 Jan 15.}
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author = {Jiang, A and Lin, J and Wang, C},
title = {{Physiological energetics of the ascidian Styela clava in relation to body size and temperature}},
journal = {COMP BIOCHEM PHYS A},
year = {2008},
volume = {149},
number = {2},
pages = {129--136},
month = feb,
annote = {Jiang, Ai-LiLin, JianWang, Chang-HaiResearch Support, Non-U.S. Gov'tUnited StatesComparative biochemistry and physiology. Part A, Molecular {\&}amp; integrative physiologyComp Biochem Physiol A Mol Integr Physiol. 2008 Feb;149(2):129-36. Epub 2007 Nov 17.}
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author = {Irmler, M and Hartl, Daniel L and Schmidt, T and Schuchhardt, Johannes and Lach, C and Meyer, H and Hrabe de Angelis, M and Klose, J and Beckers, J},
title = {{An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons}},
journal = {Proteomics},
year = {2008},
volume = {8},
number = {6},
pages = {1165--1169},
month = mar,
annote = {Irmler, MartinHartl, DanielaSchmidt, ThorstenSchuchhardt, JohannesLach, ChristianeMeyer, Helmut EHrabe de Angelis, MartinKlose, JoachimBeckers, JohannesComparative StudyResearch Support, Non-U.S. Gov'tGermanyProteomicsProteomics. 2008 Mar;8(6):1165-9.}
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author = {Hutter, Stephan and Saminadin-Peter, Sarah and Stephan, Wolfgang and Parsch, John},
title = {{Gene expression variation in African and European populations of Drosophila melanogaster}},
journal = {Genome Biology},
year = {2008},
volume = {9},
number = {1},
pages = {R12}
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author = {Hood, Leroy},
title = {{Gene regulatory networks and embryonic specification}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {16},
pages = {5951--5952},
month = apr
}
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author = {Hegreness, M and Shoresh, N and Damian, D and Hartl, Daniel L and Kishony, R},
title = {{Accelerated evolution of resistance in multidrug environments}},
journal = {Proc Natl Acad Sci USA},
year = {2008},
volume = {105},
number = {37},
pages = {13977--13981},
month = sep,
annote = {Hegreness, MatthewShoresh, NoamDamian, DorisHartl, DanielKishony, RoyR01GM081617/GM/United States NIGMSResearch Support, N.I.H., ExtramuralUnited StatesProceedings of the National Academy of Sciences of the United States of AmericaProc Natl Acad Sci U S A. 2008 Sep 16;105(37):13977-81. Epub 2008 Sep 8.}
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author = {Hartl, Daniel L and Julieron, M and LeRidant, A and Janot, F and Marandas, P and Travagli, J},
title = {{Botulinum toxin A for quality of life improvement in post-parotidectomy gustatory sweating (Frey's syndrome)}},
journal = {J Laryngol Otol},
year = {2008},
volume = {122},
number = {10},
pages = {1100--1104},
month = oct,
annote = {Hartl, D MJulieron, MLeRidant, A-MJanot, FMarandas, PTravagli, J-PEnglandThe Journal of laryngology and otologyJ Laryngol Otol. 2008 Oct;122(10):1100-4. Epub 2008 Feb 21.}
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@article{Hartl:2008fj,
author = {Hartl, Daniel L and Dauchy, S and Escande, C and Bretagne, E and Janot, F and Kolb, F},
title = {{Quality of life after free-flap tongue reconstruction}},
journal = {J Laryngol Otol},
year = {2008},
pages = {1--5},
month = sep,
annote = {Journal articleThe Journal of laryngology and otologyJ Laryngol Otol. 2008 Sep 17:1-5.}
}
@article{Hartl:2008dx,
author = {Hartl, Daniel L and Cohen, M and Julieron, M and Marandas, P and Janot, F and Bourhis, J},
title = {{Botulinum toxin for radiation-induced facial pain and trismus}},
journal = {Otolaryngol Head Neck Surg},
year = {2008},
volume = {138},
number = {4},
pages = {459--463},
month = apr,
annote = {Hartl, Dana MCohen, MyriamJulieron, MorbizeMarandas, PatrickJanot, FraneoisBourhis, JeanUnited StatesOtolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck SurgeryOtolaryngol Head Neck Surg. 2008 Apr;138(4):459-463.}
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@article{Hartl:2008ew,
author = {Hartl, Daniel L and Rohe, M and Mao, L and Staufenbiel, M and Zabel, C and Klose, J},
title = {{Impairment of adolescent hippocampal plasticity in a mouse model for Alzheimer's disease precedes disease phenotype}},
journal = {PLoS ONE},
year = {2008},
volume = {3},
number = {7},
pages = {e2759},
annote = {Hartl, DanielaRohe, MichaelMao, LeiStaufenbiel, MatthiasZabel, ClausKlose, JoachimResearch Support, Non-U.S. Gov'tUnited StatesPLoS ONEPLoS ONE. 2008 Jul 23;3(7):e2759.}
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@article{Hartl:2008hw,
author = {Hartl, Daniel L and Lehmann, N and Hoffmann, F and Jansson, A and Hector, A and Notheis, G and Roos, D and Belohradsky, B and Wintergerst, U},
title = {{Dysregulation of innate immune receptors on neutrophils in chronic granulomatous disease}},
journal = {J Allergy Clin Immunol},
year = {2008},
volume = {121},
number = {2},
pages = {375--382 e9},
month = feb,
annote = {Hartl, DominikLehmann, NatalieHoffmann, FlorianJansson, AnnetteHector, AndreasNotheis, GundulaRoos, DirkBelohradsky, Bernd HWintergerst, UweComparative StudyUnited StatesThe Journal of allergy and clinical immunologyJ Allergy Clin Immunol. 2008 Feb;121(2):375-382.e9. Epub 2007 Dec 26.}
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title = {{Infiltrated neutrophils acquire novel chemokine receptor expression and chemokine responsiveness in chronic inflammatory lung diseases}},
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year = {2008},
volume = {181},
number = {11},
pages = {8053--8067},
month = dec,
annote = {Hartl, DominikKrauss-Etschmann, SusanneKoller, BarbaraHordijk, Peter LKuijpers, Taco WHoffmann, FlorianHector, AndreasEber, ErnstMarcos, VeronicaBittmann, IrisEickelberg, OliverGriese, MatthiasRoos, DirkUnited StatesJournal of immunology (Baltimore, Md. : 1950)J Immunol. 2008 Dec 1;181(11):8053-67.}
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author = {Hartl, Daniel L and Irmler, M and Romer, I and Mader, M and Mao, L and Zabel, C and de Angelis, M and Beckers, J and Klose, J},
title = {{Transcriptome and proteome analysis of early embryonic mouse brain development}},
journal = {Proteomics},
year = {2008},
volume = {8},
number = {6},
pages = {1257--1265},
month = mar,
annote = {Hartl, DanielaIrmler, MartinRomer, IrmgardMader, Michael TMao, LeiZabel, Clausde Angelis, Martin HrabeBeckers, JohannesKlose, JoachimResearch Support, Non-U.S. Gov'tGermanyProteomicsProteomics. 2008 Mar;8(6):1257-65.}
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@article{Hartl:2008eh,
author = {Hartl, Daniel L and He, C and Koller, B and Da Silva, C and Homer, R and Lee, C and Elias, J},
title = {{Acidic Mammalian Chitinase Is Secreted via an ADAM17/Epidermal Growth Factor Receptor-dependent Pathway and Stimulates Chemokine Production by Pulmonary Epithelial Cells}},
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volume = {283},
number = {48},
pages = {33472--33482},
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annote = {Hartl, DominikHe, Chuan HuaKoller, BarbaraDa Silva, Carla AHomer, RobertLee, Chun GElias, Jack AUnited StatesThe Journal of biological chemistryJ Biol Chem. 2008 Nov 28;283(48):33472-82. Epub 2008 Sep 29.}
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author = {Hartl, Daniel L},
title = {{Immunological mechanisms behind the cystic fibrosis-ABPA link}},
journal = {Med Mycol},
year = {2008},
pages = {1--9},
month = jul,
annote = {Journal articleMedical mycology : official publication of the International Society for Human and Animal MycologyMed Mycol. 2008 Jul 24:1-9.}
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author = {Griese, M and Kappler, M and Gaggar, A and Hartl, Daniel L},
title = {{Inhibition of airway proteases in cystic fibrosis lung disease}},
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volume = {32},
number = {3},
pages = {783--795},
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author = {Gilad, Yoav and Rifkin, Scott and Pritchard, Jonathan K},
title = {{Revealing the architecture of gene regulation: the promise of eQTL studies}},
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pages = {408--415},
annote = {doi: DOI: 10.1016/j.tig.2008.06.001}
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author = {Gao, Feng and Davidson, Eric},
title = {{Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution}},
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title = {{The uptake and fate of vanadyl ion in ascidian blood cells and a detailed hypothesis for the mechanism and location of biological vanadium reduction. A visible and X-ray absorption spectroscopic study}},
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title = {{Environmentally relevant cadmium concentrations affect development and induce apoptosis of Paracentrotus lividus larvae cultured in vitro}},
journal = {Cell biology and toxicology},
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author = {Fedders, H and Leippe, M},
title = {{A reverse search for antimicrobial peptides in Ciona intestinalis: identification of a gene family expressed in hemocytes and evaluation of activity}},
journal = {CURR TOP DEV BIOL},
year = {2008},
volume = {32},
number = {3},
pages = {286--298},
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author = {Epel, D and Luckenbach, T and Stevenson, C and Macmanus-Spencer, L and Hamdoun, A and Smital, T},
title = {{Efflux transporters: newly appreciated roles in protection against pollutants}},
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volume = {42},
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author = {Dunning, Mark and Ritchie, Matthew and Barbosa-Morais, Nuno and Tavare, Simon and Lynch, Andy},
title = {{Spike-in validation of an Illumina-specific variance-stabilizing transformation}},
journal = {BMC Research Notes},
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volume = {1},
number = {1},
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author = {Dunning, Mark and Barbosa-Morais, Nuno and Lynch, Andy and Tavare, Simon and Ritchie, Matthew},
title = {{Statistical issues in the analysis of Illumina data}},
journal = {BMC Bioinformatics},
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volume = {9},
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pages = {85}
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title = {{Regulatory activity revealed by dynamic correlations in gene expression noise}},
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author = {Du, Pan and Kibbe, Warren and Lin, Simon},
title = {{lumi: a pipeline for processing Illumina microarray}},
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author = {Davidson, Eric and Levine, Michael},
title = {{Properties of developmental gene regulatory networks}},
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volume = {105},
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pages = {20063--20066},
annote = {10.1073/pnas.0806007105}