Publications for 2013

2013

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Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Genome biology Volume 14 (2013) p.R148 DOI: 10.1186/gb-2013-14-12-r148
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Reconstructing Native American migrations from whole-genome and whole-exome data.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, 1000 Genomes Project, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. PLoS genetics Volume 9 (2013) p.e1004023 DOI: 10.1371/journal.pgen.1004023
ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN. Journal of extracellular vesicles Volume 2 (2013) DOI: 10.3402/jev.v2i0.22859
Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V. Molecular systems biology Volume 9 (2013) p.714 DOI: 10.1002/msb.201304521
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. Bioinformatics (Oxford, England) Volume 30 (2014) p.1008-1009 DOI: 10.1093/bioinformatics/btt737
Archaic humans: Four makes a party.
Birney E, Pritchard JK. Nature Volume 505 (2014) p.32-34 DOI: 10.1038/nature12847
Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S. Virus research Volume 182 (2014) p.43-49 DOI: 10.1016/j.virusres.2013.12.009
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Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D. BMC systems biology Volume 7 (2013) p.139 DOI: 10.1186/1752-0509-7-139
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. PLoS computational biology Volume 9 (2013) p.e1003382 DOI: 10.1371/journal.pcbi.1003382
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Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR, Apweiler R, Ping P. Journal of proteome research Volume 13 (2014) p.433-446 DOI: 10.1021/pr400539j
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Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology.
Tee L, Lim DH, Dias RP, Baudement MO, Slater AA, Kirby G, Hancocks T, Stewart H, Hardy C, Macdonald F, Maher ER. Clinical epigenetics Volume 5 (2013) p.23 DOI: 10.1186/1868-7083-5-23
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. BMC systems biology Volume 7 (2013) p.135 DOI: 10.1186/1752-0509-7-135
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Suppression of type 1 pilus assembly in uropathogenic Escherichia coli by chemical inhibition of subunit polymerization.
Lo AW, Van de Water K, Gane PJ, Chan AW, Steadman D, Stevens K, Selwood DL, Waksman G, Remaut H. The Journal of antimicrobial chemotherapy Volume 69 (2014) p.1017-1026 DOI: 10.1093/jac/dkt467
Ensembl 2014.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Yates A, Zerbino DR, Searle SM. Nucleic acids research Volume 42 (2014) p.D749-55 DOI: 10.1093/nar/gkt1196
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. Nucleic acids research Volume 42 (2014) p.D485-9 DOI: 10.1093/nar/gkt1243
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077 DOI: 10.1093/database/bat077
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H. Nucleic acids research Volume 42 (2014) p.D1001-6 DOI: 10.1093/nar/gkt1229
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Nutrigenomics of high fat diet induced obesity in mice suggests relationships between susceptibility to fatty liver disease and the proteasome.
Waller-Evans H, Hue C, Fearnside J, Rothwell AR, Lockstone HE, Caldérari S, Wilder SP, Cazier JB, Scott J, Gauguier D. PloS one Volume 8 (2013) p.e82825 DOI: 10.1371/journal.pone.0082825
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A. Nucleic acids research Volume 42 (2014) p.D926-32 DOI: 10.1093/nar/gkt1270
iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A. Nucleic acids research Volume 42 (2014) p.D364-73 DOI: 10.1093/nar/gkt1210
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Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. Science (New York, N.Y.) Volume 342 (2013) p.1516-1517 DOI: 10.1126/science.1241130
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The Amborella genome and the evolution of flowering plants.
Amborella Genome Project. Science (New York, N.Y.) Volume 342 (2013) p.1241089 DOI: 10.1126/science.1241089
SCOP2 prototype: a new approach to protein structure mining.
Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG. Nucleic acids research Volume 42 (2014) p.D310-4 DOI: 10.1093/nar/gkt1242
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.
Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo LF, Kaleta C, Kost C. The ISME journal Volume 8 (2014) p.953-962 DOI: 10.1038/ismej.2013.211
Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Nucleic acids research Volume 42 (2014) p.D222-30 DOI: 10.1093/nar/gkt1223
Evolution of the thermopsin peptidase family (A5).
Rawlings ND. PloS one Volume 8 (2013) p.e78998 DOI: 10.1371/journal.pone.0078998
PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. Nucleic acids research Volume 42 (2014) p.D285-91 DOI: 10.1093/nar/gkt1180
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F. Nucleic acids research Volume 42 (2014) p.D873-8 DOI: 10.1093/nar/gkt1198
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LUD, a new protein domain associated with lactate utilization.
Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A. BMC bioinformatics Volume 14 (2013) p.341 DOI: 10.1186/1471-2105-14-341
Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
Marsh JA, Teichmann SA. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 36 (2014) p.209-218 DOI: 10.1002/bies.201300134
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Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya.
Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B, Campino S, Assefa S, Auburn S, Manske M, Maslen G, Peshu N, Kwiatkowski DP, Marsh K, Nzila A, Clark TG. Scientific reports Volume 3 (2013) p.3318 DOI: 10.1038/srep03318
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Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer.
Feig C, Jones JO, Kraman M, Wells RJ, Deonarine A, Chan DS, Connell CM, Roberts EW, Zhao Q, Caballero OL, Teichmann SA, Janowitz T, Jodrell DI, Tuveson DA, Fearon DT. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.20212-20217 DOI: 10.1073/pnas.1320318110
The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. Nucleic acids research Volume 42 (2014) p.D18-25 DOI: 10.1093/nar/gkt1206
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Policy challenges of clinical genome sequencing.
Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E, Firth HV. BMJ (Clinical research ed.) Volume 347 (2013) p.f6845 DOI: 10.1136/bmj.f6845
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Saccharomyces genome database provides new regulation data.
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM. Nucleic acids research Volume 42 (2014) p.D717-25 DOI: 10.1093/nar/gkt1158
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Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA. Nucleic acids research Volume 42 (2014) p.D240-5 DOI: 10.1093/nar/gkt1205
Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H. Nucleic acids research Volume 42 (2014) p.D50-2 DOI: 10.1093/nar/gkt1081
myChEMBL: a virtual machine implementation of open data and cheminformatics tools.
Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP. Bioinformatics (Oxford, England) Volume 30 (2014) p.298-300 DOI: 10.1093/bioinformatics/btt666
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Comment on on the propagation of errors by Jaskolski (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.2297 DOI: 10.1107/S090744491302917X
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Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L. BMC bioinformatics Volume 14 (2013) p.327 DOI: 10.1186/1471-2105-14-327
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Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.2296 DOI: 10.1107/S0907444913029168
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.2395-2402 DOI: 10.1107/S0907444913022294
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Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Bioinformatics (Oxford, England) Volume 30 (2014) p.165-171 DOI: 10.1093/bioinformatics/btt667
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Activities at the Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 42 (2014) p.D191-8 DOI: 10.1093/nar/gkt1140
The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. Nucleic acids research Volume 42 (2014) p.D472-7 DOI: 10.1093/nar/gkt1102
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Improving the performance of Transposable Elements detection tools.
Loureiro T, Camacho R, Vieira J, Fonseca NA. Journal of integrative bioinformatics Volume 10 (2013) p.231 DOI: 10.2390/biecoll-jib-2013-231
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. Nucleic acids research Volume 42 (2014) p.D358-63 DOI: 10.1093/nar/gkt1115
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Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa.
Chitray M, de Beer TA, Vosloo W, Maree FF. Archives of virology Volume 159 (2014) p.947-961 DOI: 10.1007/s00705-013-1838-9
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Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Nucleic acids research Volume 42 (2014) p.D917-21 DOI: 10.1093/nar/gkt1065
Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. Nucleic acids research Volume 42 (2014) p.D1193-9 DOI: 10.1093/nar/gkt1110
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Current status and new features of the Consensus Coding Sequence database.
Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Nucleic acids research Volume 42 (2014) p.D865-72 DOI: 10.1093/nar/gkt1059
Assembly information services in the European Nucleotide Archive.
Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 42 (2014) p.D38-43 DOI: 10.1093/nar/gkt1082
The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP. Nucleic acids research Volume 42 (2014) p.D1083-90 DOI: 10.1093/nar/gkt1031
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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ. G3 (Bethesda, Md.) Volume 3 (2013) p.2031-2047 DOI: 10.1534/g3.113.007153
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H. Nucleic acids research Volume 42 (2014) p.D802-9 DOI: 10.1093/nar/gkt977
A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D. Drug discovery today Volume 19 (2014) p.882-889 DOI: 10.1016/j.drudis.2013.10.024
TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A. Nucleic acids research Volume 42 (2014) p.D922-5 DOI: 10.1093/nar/gkt1055
WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW. Nucleic acids research Volume 42 (2014) p.D789-93 DOI: 10.1093/nar/gkt1063
Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J, Bertone P. Nature methods Volume 10 (2013) p.1177-1184 DOI: 10.1038/nmeth.2714
Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium. Nature methods Volume 10 (2013) p.1185-1191 DOI: 10.1038/nmeth.2722
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Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state.
Hanning JE, Saini HK, Murray MJ, Caffarel MM, van Dongen S, Ward D, Barker EM, Scarpini CG, Groves IJ, Stanley MA, Enright AJ, Pett MR, Coleman N. The Journal of pathology Volume 231 (2013) p.354-366 DOI: 10.1002/path.4244
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Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
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Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. BMC systems biology Volume 7 (2013) p.116 DOI: 10.1186/1752-0509-7-116
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The Nucleic Acid Database: new features and capabilities.
Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM. Nucleic acids research Volume 42 (2014) p.D114-22 DOI: 10.1093/nar/gkt980
The functional therapeutic chemical classification system.
Croset S, Overington JP, Rebholz-Schuhmann D. Bioinformatics (Oxford, England) Volume 30 (2014) p.876-883 DOI: 10.1093/bioinformatics/btt628
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Update of the human and mouse SERPIN gene superfamily.
Heit C, Jackson BC, McAndrews M, Wright MW, Thompson DC, Silverman GA, Nebert DW, Vasiliou V. Human genomics Volume 7 (2013) p.22 DOI: 10.1186/1479-7364-7-22
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A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1.
Danovi D, Folarin A, Gogolok S, Ender C, Elbatsh AM, Engström PG, Stricker SH, Gagrica S, Georgian A, Yu D, U KP, Harvey KJ, Ferretti P, Paddison PJ, Preston JE, Abbott NJ, Bertone P, Smith A, Pollard SM. PloS one Volume 8 (2013) p.e77053 DOI: 10.1371/journal.pone.0077053
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IMG 4 version of the integrated microbial genomes comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. Nucleic acids research Volume 42 (2014) p.D560-7 DOI: 10.1093/nar/gkt963
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA. Nucleic acids research Volume 42 (2014) p.D600-6 DOI: 10.1093/nar/gkt961
Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM. Nucleic acids research Volume 42 (2014) p.D546-52 DOI: 10.1093/nar/gkt979
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A. Nucleic acids research Volume 42 (2014) p.D503-9 DOI: 10.1093/nar/gkt953
PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA. Nucleic acids research Volume 42 (2014) p.D292-6 DOI: 10.1093/nar/gkt940
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The role of reporting standards for metabolite annotation and identification in metabolomic studies.
Salek RM, Steinbeck C, Viant MR, Goodacre R, Dunn WB. GigaScience Volume 2 (2013) p.13 DOI: 10.1186/2047-217x-2-13
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IMG/M 4 version of the integrated metagenome comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. Nucleic acids research Volume 42 (2014) p.D568-73 DOI: 10.1093/nar/gkt919
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Smoothing 3D protein structure motifs through graph mining and amino acid similarities.
Dhifli W, Saidi R, Nguifo EM. Journal of computational biology : a journal of computational molecular cell biology Volume 21 (2014) p.162-172 DOI: 10.1089/cmb.2013.0092
An estimated 5% of new protein structures solved today represent a new Pfam family.
Mistry J, Kloppmann E, Rost B, Punta M. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.2186-2193 DOI: 10.1107/S0907444913027157
*
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Li C, Jimeno Yepes A, Hoehndorf R, Backofen R, Lewin I. Journal of biomedical semantics Volume 4 (2013) p.28 DOI: 10.1186/2041-1480-4-28
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J. Journal of biomedical semantics Volume 4 (2013) p.20 DOI: 10.1186/2041-1480-4-20
From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R. Briefings in functional genomics Volume 12 (2013) p.471-482 DOI: 10.1093/bfgp/elt033
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ. Journal of structural biology Volume 184 (2013) p.173-181 DOI: 10.1016/j.jsb.2013.09.021
*
Biomarkers in autism spectrum disorder: the old and the new.
Ruggeri B, Sarkans U, Schumann G, Persico AM. Psychopharmacology Volume 231 (2014) p.1201-1216 DOI: 10.1007/s00213-013-3290-7
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).
Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I. PloS one Volume 8 (2013) p.e75185 DOI: 10.1371/journal.pone.0075185
*
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. PLoS computational biology Volume 9 (2013) p.e1003253 DOI: 10.1371/journal.pcbi.1003253
CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system.
Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG. Cell reports Volume 5 (2013) p.271-282 DOI: 10.1016/j.celrep.2013.09.001
*
Estimating error rates in bioactivity databases.
Tiikkainen P, Bellis L, Light Y, Franke L. Journal of chemical information and modeling Volume 53 (2013) p.2499-2505 DOI: 10.1021/ci400099q
Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. Proteomics Volume 13 (2013) p.2931-2937 DOI: 10.1002/pmic.201370166
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Science (New York, N.Y.) Volume 342 (2013) p.1235587 DOI: 10.1126/science.1235587
*
A long road towards the structure of respiratory complex I, a giant molecular proton pump.
Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G. Biochemical Society transactions Volume 41 (2013) p.1265-1271 DOI: 10.1042/bst20130193
*
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Nature genetics Volume 45 (2013) p.1353-1360 DOI: 10.1038/ng.2770
Capturing cooperative interactions with the PSI-MI format.
Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat066 DOI: 10.1093/database/bat066
*
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A. Journal of cheminformatics Volume 5 (2013) p.42 DOI: 10.1186/1758-2946-5-42
BioServices: a common Python package to access biological Web Services programmatically.
Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 29 (2013) p.3241-3242 DOI: 10.1093/bioinformatics/btt547
Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. Nature methods Volume 10 (2013) p.1093-1095 DOI: 10.1038/nmeth.2645
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Mirlach F, Saez-Rodriguez J. F1000Research Volume 2 (2013) p.192 DOI: 10.12688/f1000research.2-192.v2
*
Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM. PLoS genetics Volume 9 (2013) p.e1003803 DOI: 10.1371/journal.pgen.1003803
*
Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.
Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L. Evolution; international journal of organic evolution Volume 68 (2014) p.605-613 DOI: 10.1111/evo.12262
*
HIV-1 uncoating in human CD4+ T cells: kinetic and functional analyses.
Chen N, Zhou L, Gane PG, Price A, Zufferey M, Luban J, James L, Selwood D, Fassati A. Retrovirology Volume 10 (2013) p.P13-P13 DOI: 10.1186/1742-4690-10-S1-P13
ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. PLoS computational biology Volume 9 (2013) p.e1003242 DOI: 10.1371/journal.pcbi.1003242
*
Organizing a PhD symposium--an inside view. Setting up a scientific meeting is challenging--a PhD symposium offers its own unique opportunities and pitfalls.
Schröder MS, Harnett D, Minke BA, Nair PS, Committee Member Consortium. EMBO reports Volume 14 (2013) p.856-860 DOI: 10.1038/embor.2013.147
*
A variant in LDLR is associated with abdominal aortic aneurysm.
Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K, Child AH, Clough RE, Cockerill G, Hafez H, Scott DJ, Ariëns RA, Johnson A, Sohrabi S, Smith A, Thompson MM, van Bockxmeer FM, Waltham M, Matthíasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Wild JB, Edkins S, Gwilliam R, Hunt SE, Potter S, Lindholt JS, Golledge J, Norman PE, van Rij A, Powell JT, Eriksson P, Stefánsson K, Thompson JR, Humphries SE, Sayers RD, Deloukas P, Samani NJ, Bown MJ. Circulation. Cardiovascular genetics Volume 6 (2013) p.498-504 DOI: 10.1161/circgenetics.113.000165
*
Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET. Nature Volume 501 (2013) p.506-511 DOI: 10.1038/nature12531
*
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T. Nature biotechnology Volume 31 (2013) p.1015-1022 DOI: 10.1038/nbt.2702
*
Monitoring named entity recognition: the League Table.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Jimeno Yepes A, Lewin I. Journal of biomedical semantics Volume 4 (2013) p.19 DOI: 10.1186/2041-1480-4-19
OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2955-2957 DOI: 10.1093/bioinformatics/btt514
*
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A. BMC bioinformatics Volume 14 (2013) p.265 DOI: 10.1186/1471-2105-14-265
*
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M. Genome research Volume 23 (2013) p.2066-2077 DOI: 10.1101/gr.161620.113
Exploiting disjointness axioms to improve semantic similarity measures.
Ferreira JD, Hastings J, Couto FM. Bioinformatics (Oxford, England) Volume 29 (2013) p.2781-2787 DOI: 10.1093/bioinformatics/btt491
*
How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Structure (London, England : 1993) Volume 21 (2013) p.1485-1491 DOI: 10.1016/j.str.2013.07.010
*
The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.
i5K Consortium. The Journal of heredity Volume 104 (2013) p.595-600 DOI: 10.1093/jhered/est050
*
Recommendations of the wwPDB NMR Validation Task Force.
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Structure (London, England : 1993) Volume 21 (2013) p.1563-1570 DOI: 10.1016/j.str.2013.07.021
*
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.
Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. Genome biology Volume 14 (2013) p.R88 DOI: 10.1186/gb-2013-14-8-r88
*
Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL, Kariuki S. Current microbiology Volume 68 (2014) p.64-70 DOI: 10.1007/s00284-013-0447-x
*
The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. PLoS biology Volume 11 (2013) p.e1001638 DOI: 10.1371/journal.pbio.1001638
*
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat062 DOI: 10.1093/database/bat062
*
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Lee SH, Magnusson PK, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Psychosis Endophenotypes International Consortium, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Wellcome Trust Case Control Consortium 2, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CC, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CC, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF. Nature genetics Volume 45 (2013) p.1150-1159 DOI: 10.1038/ng.2742
*
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Proteins Volume 81 (2013) p.1980-1987 DOI: 10.1002/prot.24356
*
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Petrov AI, Zirbel CL, Leontis NB. RNA Volume 19 (2013) p.1327-1340 DOI: 10.1261/rna.039438.113
*
Association of gut microbiota with post-operative clinical course in Crohn's disease.
Dey N, Soergel DA, Repo S, Brenner SE. BMC gastroenterology Volume 13 (2013) p.131 DOI: 10.1186/1471-230X-13-131
KNIME-CDK: Workflow-driven cheminformatics.
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C. BMC bioinformatics Volume 14 (2013) p.257 DOI: 10.1186/1471-2105-14-257
*
Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P. Circulation research Volume 113 (2013) p.1043-1053 DOI: 10.1161/CIRCRESAHA.113.301151
A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium. Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809 DOI: 10.1093/bioinformatics/btt484
*
Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.
Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L. PLoS genetics Volume 9 (2013) p.e1003730 DOI: 10.1371/journal.pgen.1003730
*
Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.
Martello G, Bertone P, Smith A. The EMBO journal Volume 32 (2013) p.2561-2574 DOI: 10.1038/emboj.2013.177
*
Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons.
Fabbro A, Sucapane A, Toma FM, Calura E, Rizzetto L, Carrieri C, Roncaglia P, Martinelli V, Scaini D, Masten L, Turco A, Gustincich S, Prato M, Ballerini L. PloS one Volume 8 (2013) p.e73621 DOI: 10.1371/journal.pone.0073621
*
Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.
Hamilton-Williams EE, Rainbow DB, Cheung J, Christensen M, Lyons PA, Peterson LB, Steward CA, Sherman LA, Wicker LS. Mammalian genome : official journal of the International Mammalian Genome Society Volume 24 (2013) p.358-375 DOI: 10.1007/s00335-013-9466-y
Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM. eLife Volume 2 (2013) p.e00522 DOI: 10.7554/eLife.00522
*
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cell Volume 154 (2013) p.530-540 DOI: 10.1016/j.cell.2013.07.007
*
Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R. Scandinavian journal of immunology Volume 78 (2013) p.172-180 DOI: 10.1111/sji.12071
*
Evolutionary biology: The handiwork of tinkering.
Flicek P. Nature Volume 500 (2013) p.158-159 DOI: 10.1038/500158a
*
Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Nature methods Volume 10 (2013) p.723-729 DOI: 10.1038/nmeth.2562
*
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. BMC genomics Volume 14 (2013) p.513 DOI: 10.1186/1471-2164-14-513
*
DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT.
Schneider L, Pellegatta S, Favaro R, Pisati F, Roncaglia P, Testa G, Nicolis SK, Finocchiaro G, d'Adda di Fagagna F. Stem cell reports Volume 1 (2013) p.123-138 DOI: 10.1016/j.stemcr.2013.06.004
Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA. Current opinion in structural biology Volume 23 (2013) p.954-963 DOI: 10.1016/j.sbi.2013.07.004
*
Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY. American journal of human genetics Volume 93 (2013) p.236-248 DOI: 10.1016/j.ajhg.2013.06.011
*
Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. Cell Volume 154 (2013) p.691-703 DOI: 10.1016/j.cell.2013.06.040
*
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP. BMC bioinformatics Volume 14 (2013) p.235 DOI: 10.1186/1471-2105-14-235
Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ. International journal of molecular sciences Volume 14 (2013) p.15423-15458 DOI: 10.3390/ijms140815423
*
Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE. British journal of cancer Volume 109 (2013) p.983-993 DOI: 10.1038/bjc.2013.396
*
An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A. Journal of biomolecular NMR Volume 58 (2014) p.259-285 DOI: 10.1007/s10858-013-9750-x
*
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. GigaScience Volume 2 (2013) p.10 DOI: 10.1186/2047-217x-2-10
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM. Aging cell Volume 12 (2013) p.917-922 DOI: 10.1111/acel.12123
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Ziehm M, Thornton JM. Aging cell Volume 12 (2013) p.910-916 DOI: 10.1111/acel.12121
*
A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M, Psychiatric Genomics Consortium, Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC. Biological psychiatry Volume 75 (2014) p.386-397 DOI: 10.1016/j.biopsych.2013.03.033
*
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 29 (2013) p.2320-2326 DOI: 10.1093/bioinformatics/btt393
*
The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.
Hall Z, Hernández H, Marsh JA, Teichmann SA, Robinson CV. Structure (London, England : 1993) Volume 21 (2013) p.1325-1337 DOI: 10.1016/j.str.2013.06.004
*
JBioWH: an open-source Java framework for bioinformatics data integration.
Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat051 DOI: 10.1093/database/bat051
*
Tetrazole-based deoxyamodiaquines: synthesis, ADME/PK profiling and pharmacological evaluation as potential antimalarial agents.
Tukulula M, Njoroge M, Mugumbate GC, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Heudi O, Kameni-Tcheudji J, Chibale K. Bioorganic & medicinal chemistry Volume 21 (2013) p.4904-4913 DOI: 10.1016/j.bmc.2013.06.067
*
SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.
Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K. Journal of proteomics Volume 91 (2013) p.164-171 DOI: 10.1016/j.jprot.2013.06.033
The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 2 (2013) p.e54 DOI: 10.1038/psp.2013.30
The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.
Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND. F1000Research Volume 2 (2013) p.154 DOI: 10.12688/f1000research.2-154.v2
*
A guide to best practices for Gene Ontology (GO) manual annotation.
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat054 DOI: 10.1093/database/bat054
*
The evolution of the Anopheles 16 genomes project.
Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ. G3 (Bethesda, Md.) Volume 3 (2013) p.1191-1194 DOI: 10.1534/g3.113.006247
*
Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.
Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consortium 2 (WTCCC2). Human molecular genetics Volume 22 (2013) p.4653-4660 DOI: 10.1093/hmg/ddt293
*
Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Sanger Institute Mouse Genetics Project, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP. Cell Volume 154 (2013) p.452-464 DOI: 10.1016/j.cell.2013.06.022
*
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R. The Journal of pathology Volume 230 (2013) p.270-276 DOI: 10.1002/path.4209
*
Correction.
Journal of the American Chemical Society Volume 135 (2013) p.10178 DOI: 10.1021/ja403136h
*
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Genome biology Volume 14 (2013) p.R70 DOI: 10.1186/gb-2013-14-7-r70
Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Methods (San Diego, Calif.) Volume 63 (2013) p.41-49 DOI: 10.1016/j.ymeth.2013.06.027
*
Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Molecular & cellular proteomics : MCP Volume 12 (2013) p.3026-3035 DOI: 10.1074/mcp.o113.029777
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM. BMC systems biology Volume 7 (2013) p.52 DOI: 10.1186/1752-0509-7-52
*
Best practices in bioinformatics training for life scientists.
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. Briefings in bioinformatics Volume 14 (2013) p.528-537 DOI: 10.1093/bib/bbt043
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PAF, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FMK, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor B, Trabzuni D, North American Brain Expression Consortium, UK Brain Expression Consortium, Rossin E, Lage K, Jacobs SBR, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AMJM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman D, Palotie A. Nature genetics Volume 45 (2013) p.912-917 DOI: 10.1038/ng.2676
*
Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC. Journal of proteomics Volume 89 (2013) p.179-182 DOI: 10.1016/j.jprot.2013.06.013
*
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. Briefings in bioinformatics Volume 14 (2013) p.548-555 DOI: 10.1093/bib/bbt045
*
Polymer models of chromatin organization.
Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M. Frontiers in Genetics Volume 4 (2013) p.113 DOI: 10.3389/fgene.2013.00113
*
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Immunity Volume 38 (2013) p.1271-1284 DOI: 10.1016/j.immuni.2013.05.011
*
ISMB/ECCB 2013 Proceedings Papers Committee.
Bioinformatics (Oxford, England) Volume 29 (2013) p.i3-i8 DOI: 10.1093/bioinformatics/btt281
*
Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.
Mancini C, Roncaglia P, Brussino A, Stevanin G, Lo Buono N, Krmac H, Maltecca F, Gazzano E, Bartoletti Stella A, Calvaruso MA, Iommarini L, Cagnoli C, Forlani S, Le Ber I, Durr A, Brice A, Ghigo D, Casari G, Porcelli AM, Funaro A, Gasparre G, Gustincich S, Brusco A. BMC medical genomics Volume 6 (2013) p.22 DOI: 10.1186/1755-8794-6-22
*
LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
Murray MJ, Saini HK, Siegler CA, Hanning JE, Barker EM, van Dongen S, Ward DM, Raby KL, Groves IJ, Scarpini CG, Pett MR, Thornton CM, Enright AJ, Nicholson JC, Coleman N, CCLG. Cancer research Volume 73 (2013) p.4872-4884 DOI: 10.1158/0008-5472.CAN-12-2085
*
Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.
Carss KJ, Stevens E, Foley AR, Cirak S, Riemersma M, Torelli S, Hoischen A, Willer T, van Scherpenzeel M, Moore SA, Messina S, Bertini E, Bönnemann CG, Abdenur JE, Grosmann CM, Kesari A, Punetha J, Quinlivan R, Waddell LB, Young HK, Wraige E, Yau S, Brodd L, Feng L, Sewry C, MacArthur DG, North KN, Hoffman E, Stemple DL, Hurles ME, van Bokhoven H, Campbell KP, Lefeber DJ, UK10K Consortium, Lin YY, Muntoni F. American journal of human genetics Volume 93 (2013) p.29-41 DOI: 10.1016/j.ajhg.2013.05.009
Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2213-2215 DOI: 10.1093/bioinformatics/btt342
*
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia.
Mellars P, Gori KC, Carr M, Soares PA, Richards MB. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.10699-10704 DOI: 10.1073/pnas.1306043110
*
Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes.
Gendrel AV, Tang YA, Suzuki M, Godwin J, Nesterova TB, Greally JM, Heard E, Brockdorff N. Molecular and cellular biology Volume 33 (2013) p.3150-3165 DOI: 10.1128/mcb.00145-13
*
Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF.
Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA. Human molecular genetics Volume 22 (2013) p.4180-4193 DOI: 10.1093/hmg/ddt265
*
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J. Nature methods Volume 10 (2013) p.676-682 DOI: 10.1038/nmeth.2519
bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC. BMC bioinformatics Volume 14 (2013) p.185 DOI: 10.1186/1471-2105-14-185
*
Selection of human tissue-specific elementary flux modes using gene expression data.
Rezola A, Pey J, de Figueiredo LF, Podhorski A, Schuster S, Rubio A, Planes FJ. Bioinformatics Volume 29 (2013) p.2009-2016 DOI: 10.1093/bioinformatics/btt328
iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. Bioinformatics (Oxford, England) Volume 29 (2013) p.1919-1921 DOI: 10.1093/bioinformatics/btt306
*
Brood parasitism correlates with the strength of spatial autocorrelation of life history and defensive traits in Magpies.
Soler JJ, Martín-Gálvez D, de Neve L, Soler M. Ecology. Volume 94 (2013) p.1338-1346 DOI: 10.1890/12-1350.1
*
Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.
Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Structure (London, England : 1993) Volume 21 (2013) p.875-881 DOI: 10.1016/j.str.2013.04.020
*
LifeTrain: towards a European framework for continuing professional development in biomedical sciences
Brooksbank C. Nature reviews. Drug discovery (2013) DOI: 10.1038/nrd4026
The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M. Database: The Journal of Biological Databases and Curation Volume 2013 (2013)
Database citation in full text biomedical articles.
Kafkas Ş, Kim JH, McEntyre JR. PloS one Volume 8 (2013) p.e63184 DOI: 10.1371/journal.pone.0063184
*
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL. Nucleic acids research Volume 41 (2013) p.W15-21 DOI: 10.1093/nar/gkt417
*
Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia.
Roberts EW, Deonarine A, Jones JO, Denton AE, Feig C, Lyons SK, Espeli M, Kraman M, McKenna B, Wells RJ, Zhao Q, Caballero OL, Larder R, Coll AP, O'Rahilly S, Brindle KM, Teichmann SA, Tuveson DA, Fearon DT. The Journal of experimental medicine Volume 210 (2013) p.1137-1151 DOI: 10.1084/jem.20122344
*
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J. Nature genetics Volume 45 (2013) p.767-775 DOI: 10.1038/ng.2644
*
Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. Current opinion in structural biology Volume 23 (2013) p.443-450 DOI: 10.1016/j.sbi.2013.03.006
*
Analysis of SAT type foot-and-mouth disease virus capsid proteins and the identification of putative amino acid residues affecting virus stability.
Maree FF, Blignaut B, de Beer TA, Rieder E. PloS one Volume 8 (2013) p.e61612 DOI: 10.1371/journal.pone.0061612
*
Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling.
Invergo BM, Montanucci L, Koch KW, Bertranpetit J, Dell'orco D. Cell communication and signaling : CCS Volume 11 (2013) p.36 DOI: 10.1186/1478-811X-11-36
*
Noncanonical expression of caudal during early embryogenesis in the pea aphid Acyrthosiphon pisum: maternal cad-driven posterior development is not conserved.
Chang CC, Hsiao YM, Huang TY, Cook CE, Shigenobu S, Chang TH. Insect molecular biology Volume 22 (2013) p.442-455 DOI: 10.1111/imb.12035
*
Scientific competency questions as the basis for semantically enriched open pharmacological space development.
Azzaoui K, Jacoby E, Senger S, Rodríguez EC, Loza M, Zdrazil B, Pinto M, Williams AJ, de la Torre V, Mestres J, Pastor M, Taboureau O, Rarey M, Chichester C, Pettifer S, Blomberg N, Harland L, Williams-Jones B, Ecker GF. Drug discovery today Volume 18 (2013) p.843-852 DOI: 10.1016/j.drudis.2013.05.008
Dissemination of metabolomics results: role of MetaboLights and COSMOS.
Salek RM, Haug K, Steinbeck C. GigaScience Volume 2 (2013) p.8 DOI: 10.1186/2047-217X-2-8
*
The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.
Araújo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, Macedo-Ribeiro S, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Vieira J. PloS one Volume 8 (2013) p.e63747 DOI: 10.1371/journal.pone.0063747
*
Structural and functional annotation of the porcine immunome.
Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK. BMC genomics Volume 14 (2013) p.332 DOI: 10.1186/1471-2164-14-332
*
Update on the Kelch-like (KLHL) gene family.
Dhanoa BS, Cogliati T, Satish AG, Bruford EA, Friedman JS. Human genomics Volume 7 (2013) p.13 DOI: 10.1186/1479-7364-7-13
Elucidating human phosphatase-substrate networks.
Li X, Wilmanns M, Thornton J, Köhn M. Science signaling Volume 6 (2013) p.rs10 DOI: 10.1126/scisignal.2003203
A new reference implementation of the PSICQUIC web service.
del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H. Nucleic acids research Volume 41 (2013) p.W601-6 DOI: 10.1093/nar/gkt392
Analysis Tool Web Services from the EMBL-EBI.
McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. Nucleic acids research Volume 41 (2013) p.W597-600 DOI: 10.1093/nar/gkt376
*
The ChEMBL database as linked open data.
Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ. Journal of cheminformatics Volume 5 (2013) p.23 DOI: 10.1186/1758-2946-5-23
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA. PloS one Volume 8 (2013) p.e61951 DOI: 10.1371/journal.pone.0061951
*
High-resolution analysis of cis-acting regulatory networks at the α-globin locus.
Hughes JR, Lower KM, Dunham I, Taylor S, De Gobbi M, Sloane-Stanley JA, McGowan S, Ragoussis J, Vernimmen D, Gibbons RJ, Higgs DR. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 368 (2013) p.20120361 DOI: 10.1098/rstb.2012.0361
Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D. Molecular cell Volume 50 (2013) p.601-608 DOI: 10.1016/j.molcel.2013.04.026
*
Vive la différence: naming structural variants in the human reference genome.
Seal RL, Wright MW, Gray KA, Bruford EA. Human genomics Volume 7 (2013) p.12 DOI: 10.1186/1479-7364-7-12
*
Characterization of a versatile organometallic pro-drug (CORM) for experimental CO based therapeutics.
Seixas JD, Mukhopadhyay A, Santos-Silva T, Otterbein LE, Gallo DJ, Rodrigues SS, Guerreiro BH, Gonçalves AM, Penacho N, Marques AR, Coelho AC, Reis PM, Romão MJ, Romão CC. Dalton transactions (Cambridge, England : 2003) Volume 42 (2013) p.5985-5998 DOI: 10.1039/c2dt32174b
*
World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA.
Baylis SA, Blümel J, Mizusawa S, Matsubayashi K, Sakata H, Okada Y, Nübling CM, Hanschmann KM, HEV Collaborative Study Group. Emerging infectious diseases Volume 19 (2013) p.729-735 DOI: 10.3201/eid1905.121845
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.
Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J. PloS one Volume 8 (2013) p.e61318 DOI: 10.1371/journal.pone.0061318
IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
Kurbatova N, Chartier M, Zylber MI, Najmanovich R. F1000Research Volume 2 (2013) p.117 DOI: 10.12688/f1000research.2-117.v2
The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat029 DOI: 10.1093/database/bat029
*
Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.
Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR. Genome biology Volume 14 (2013) p.R37 DOI: 10.1186/gb-2013-14-4-r37
*
Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.
Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM, Duong S, Nguon C, Chuor CM, Saunders D, Se Y, Lon C, Fukuda MM, Amenga-Etego L, Hodgson AV, Asoala V, Imwong M, Takala-Harrison S, Nosten F, Su XZ, Ringwald P, Ariey F, Dolecek C, Hien TT, Boni MF, Thai CQ, Amambua-Ngwa A, Conway DJ, Djimdé AA, Doumbo OK, Zongo I, Ouedraogo JB, Alcock D, Drury E, Auburn S, Koch O, Sanders M, Hubbart C, Maslen G, Ruano-Rubio V, Jyothi D, Miles A, O'Brien J, Gamble C, Oyola SO, Rayner JC, Newbold CI, Berriman M, Spencer CC, McVean G, Day NP, White NJ, Bethell D, Dondorp AM, Plowe CV, Fairhurst RM, Kwiatkowski DP. Nature genetics Volume 45 (2013) p.648-655 DOI: 10.1038/ng.2624
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N. Nature genetics Volume 45 (2013) p.701-706 DOI: 10.1038/ng.2615
Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.
Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM. Molecular bioSystems Volume 9 (2013) p.1756-1764 DOI: 10.1039/c3mb25485b
*
miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs.
Lupini L, Bassi C, Ferracin M, Bartonicek N, D'Abundo L, Zagatti B, Callegari E, Musa G, Moshiri F, Gramantieri L, Corrales FJ, Enright AJ, Sabbioni S, Negrini M. Frontiers in genetics Volume 4 (2013) p.64 DOI: 10.3389/fgene.2013.00064
*
Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.
Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, Martin P, Comeau ME, Sajuthi S, Andrews R, Brown M, Chen WM, Concannon P, Deloukas P, Edkins S, Eyre S, Gaffney PM, Guthery SL, Guthridge JM, Hunt SE, James JA, Keddache M, Moser KL, Nigrovic PA, Onengut-Gumuscu S, Onslow ML, Rosé CD, Rich SS, Steel KJ, Wakeland EK, Wallace CA, Wedderburn LR, Woo P, Boston Children's JIA Registry, British Society of Paediatric and Adolescent Rheumatology (BSPAR) Study Group, Childhood Arthritis Prospective Study (CAPS), Childhood Arthritis Response to Medication Study (CHARMS), German Society for Pediatric Rheumatology (GKJR), JIA Gene Expression Study, NIAMS JIA Genetic Registry, TREAT Study, United Kingdom Juvenile Idiopathic Arthritis Genetics Consortium (UKJIAGC), Bohnsack JF, Haas JP, Glass DN, Langefeld CD, Thomson W, Thompson SD. Nature genetics Volume 45 (2013) p.664-669 DOI: 10.1038/ng.2614
From Peptidome to PRIDE: public proteomics data migration at a large scale.
Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H. Proteomics Volume 13 (2013) p.1692-1695 DOI: 10.1002/pmic.201200514
The role of structural bioinformatics resources in the era of integrative structural biology.
Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ. Acta Crystallographica Section D: Biological Crystallography Volume 69 (2013) p.710-721 DOI: 10.1107/S0907444913001157
*
Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Raspé O, Vieira CP. Journal of experimental botany Volume 64 (2013) p.2423-2434 DOI: 10.1093/jxb/ert098
The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat023 DOI: 10.1093/database/bat023
*
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR. Molecular & cellular proteomics : MCP Volume 12 (2013) p.2332-2340 DOI: 10.1074/mcp.o113.028506
*
Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.
Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L. Journal of proteomics Volume 95 (2013) p.89-92 DOI: 10.1016/j.jprot.2013.04.011
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Nucleic acids research Volume 41 (2013) p.e121 DOI: 10.1093/nar/gkt263
*
The zebrafish reference genome sequence and its relationship to the human genome.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL. Nature Volume 496 (2013) p.498-503 DOI: 10.1038/nature12111
*
Systematic analysis of experimental phenotype data reveals gene functions.
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. PloS one Volume 8 (2013) p.e60847 DOI: 10.1371/journal.pone.0060847
*
A decadal view of biodiversity informatics: challenges and priorities.
Hardisty A, Roberts D, Biodiversity Informatics Community, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, Ariño AH, Arvanitidis C, Backeljau T, Bailly N, Belbin L, Berendsohn W, Bertrand N, Caithness N, Campbell D, Cochrane G, Conruyt N, Culham A, Damgaard C, Davies N, Fady B, Faulwetter S, Feest A, Field D, Garnier E, Geser G, Gilbert J, Grosche, Grosser D, Hardisty A, Herbinet B, Hobern D, Jones A, de Jong Y, King D, Knapp S, Koivula H, Los W, Meyer C, Morris RA, Morrison N, Morse D, Obst M, Pafilis E, Page LM, Page R, Pape T, Parr C, Paton A, Patterson D, Paymal E, Penev L, Pollet M, Pyle R, von Raab-Straube E, Robert V, Roberts D, Robertson T, Rovellotti O, Saarenmaa H, Schalk P, Schaminee J, Schofield P, Sier A, Sierra S, Smith V, van Spronsen E, Thornton-Wood S, van Tienderen P, van Tol J, Tuama ÉÓ, Uetz P, Vaas L, Vignes Lebbe R, Vision T, Vu D, De Wever A, White R, Willis K, Young F. BMC ecology Volume 13 (2013) p.16 DOI: 10.1186/1472-6785-13-16
Towards the collaborative curation of the registry underlying Identifiers.org.
Juty N, Le Novère N, Hermjakob H, Laibe C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat017 DOI: 10.1093/database/bat017
*
Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G. Nucleic acids research Volume 41 (2013) p.5189-5198 DOI: 10.1093/nar/gkt211
*
Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.
Paul DS, Albers CA, Rendon A, Voss K, Stephens J, HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P. Genome research Volume 23 (2013) p.1130-1141 DOI: 10.1101/gr.155127.113
*
Structure-based identification of OATP1B1/3 inhibitors.
De Bruyn T, van Westen GJ, Ijzerman AP, Stieger B, de Witte P, Augustijns PF, Annaert PP. Molecular pharmacology Volume 83 (2013) p.1257-1267 DOI: 10.1124/mol.112.084152
SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Silljé HHW, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA. Nature genetics Volume 45 (2013) p.542-545 DOI: 10.1038/ng.2603
*
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson WO, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimäki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt MF, Mohlke KL, O'Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E. Nature genetics Volume 45 (2013) p.501-512 DOI: 10.1038/ng.2606
*
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
Lahti L, Torrente A, Elo LL, Brazma A, Rung J. Nucleic acids research Volume 41 (2013) p.e110 DOI: 10.1093/nar/gkt229
*
Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O. Bioinformatics (Oxford, England) Volume 29 (2013) p.1382-1389 DOI: 10.1093/bioinformatics/btt148
*
Shorthand notation for lipid structures derived from mass spectrometry.
Liebisch G, Vizcaíno JA, Köfeler H, Trötzmüller M, Griffiths WJ, Schmitz G, Spener F, Wakelam MJ. Journal of lipid research Volume 54 (2013) p.1523-1530 DOI: 10.1194/jlr.m033506
Protein complexes are under evolutionary selection to assemble via ordered pathways.
Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA. Cell Volume 153 (2013) p.461-470 DOI: 10.1016/j.cell.2013.02.044
*
The ABCs of membrane transporters in health and disease (SLC series): introduction.
Hediger MA, Clémençon B, Burrier RE, Bruford EA. Molecular aspects of medicine Volume 34 (2013) p.95-107 DOI: 10.1016/j.mam.2012.12.009
*
Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project.
Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JA, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY. Human mutation Volume 34 (2013) p.661-666 DOI: 10.1002/humu.22293
The challenges of delivering bioinformatics training in the analysis of high-throughput data.
Carvalho BS, Rustici G. Briefings in bioinformatics Volume 14 (2013) p.538-547 DOI: 10.1093/bib/bbt018
*
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.
Watson-Haigh NS, Shang CA, Haimel M, Kostadima M, Loos R, Deshpande N, Duesing K, Li X, McGrath A, McWilliam S, Michnowicz S, Moolhuijzen P, Quenette S, Revote JN, Tyagi S, Schneider MV. Briefings in bioinformatics Volume 14 (2013) p.563-574 DOI: 10.1093/bib/bbt022
*
Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.
Wallach T, Schellenberg K, Maier B, Kalathur RK, Porras P, Wanker EE, Futschik ME, Kramer A. PLoS genetics Volume 9 (2013) p.e1003398 DOI: 10.1371/journal.pgen.1003398
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K, Klamt S, Rocha M, Saez-Rodriguez J. Molecular bioSystems Volume 9 (2013) p.1576-1583 DOI: 10.1039/c3mb25489e
*
Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I. BMC bioinformatics Volume 14 (2013) p.104 DOI: 10.1186/1471-2105-14-104
*
FMCS: a novel algorithm for the multiple MCS problem.
Dalke A, Hastings J. Journal of cheminformatics Volume 5 (2013) p.O6-O6 DOI: 10.1186/1758-2946-5-S1-O6
Expanding natural product chemistry resources at the EBI.
Hastings J, Conesa P, Dekker A, Ennis M, Haug K, Jayaseelan K, Kale N, Mahendraker T, Moreno P, Muthukrishnan V, Owen G, Salek R, Turner S, Steinbeck C. Journal of cheminformatics Volume 5 (2013) p.P43-P43 DOI: 10.1186/1758-2946-5-S1-P43
Data standardization and sharing-the work of the HUPO-PSI.
Orchard S. Biochimica et biophysica acta Volume 1844 (2014) p.82-87 DOI: 10.1016/j.bbapap.2013.03.011
*
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V. Analytical chemistry Volume 85 (2013) p.3515-3520 DOI: 10.1021/ac303239g
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.
de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R, Steinbeck C. BMC bioinformatics Volume 14 (2013) p.103 DOI: 10.1186/1471-2105-14-103
Brain: biomedical knowledge manipulation.
Croset S, Overington JP, Rebholz-Schuhmann D. Bioinformatics (Oxford, England) Volume 29 (2013) p.1238-1239 DOI: 10.1093/bioinformatics/btt109
*
HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D. Bioinformatics (Oxford, England) Volume 29 (2013) p.1341-1342 DOI: 10.1093/bioinformatics/btt128
*
High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.
Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IR, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AW, Preston SA, Ekblom R, Slate J, Burke T. BMC genomics Volume 14 (2013) p.176 DOI: 10.1186/1471-2164-14-176
*
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M, HUPO-PSI Group. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat009 DOI: 10.1093/database/bat009
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P. Bioinformatics (Oxford, England) Volume 29 (2013) p.1325-1332 DOI: 10.1093/bioinformatics/btt113
*
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G. Genome research Volume 23 (2013) p.749-761 DOI: 10.1101/gr.148718.112
*
A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T. Journal of internal medicine Volume 274 (2013) p.67-76 DOI: 10.1111/joim.12048
*
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. Nucleic acids research Volume 41 (2013) p.4549-4564 DOI: 10.1093/nar/gkt148
*
A community-driven global reconstruction of human metabolism.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. Nature biotechnology Volume 31 (2013) p.419-425 DOI: 10.1038/nbt.2488
*
Drug metabolite generation using a laboratory evolved NADPH independent cytochrome P450: application of in vitro and in silico approaches.
Chigorimbo-Murefu NT, Njoroge M, Louw S, Mugumbate G, Chibale K. Drug metabolism letters Volume 7 (2013) p.68-77 DOI: 10.2174/18723128112069990014
*
Implication of a rare deletion at distal 16p11.2 in schizophrenia.
Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O'Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O'Donovan MC, Lencz T, Kirov G, Molecular Genetics of Schizophrenia Consortium, Wellcome Trust Case Control Consortium 2. JAMA psychiatry Volume 70 (2013) p.253-260 DOI: 10.1001/2013.jamapsychiatry.71
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.
Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA. Biochimica et biophysica acta Volume 1844 (2014) p.63-76 DOI: 10.1016/j.bbapap.2013.02.032
*
Response to Diaz.
Bögershausen N, Bruford E, Wollnik B. Clinical genetics Volume 83 (2013) p.296 DOI: 10.1111/cge.12099
*
A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.
Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M. American journal of human genetics Volume 92 (2013) p.460-467 DOI: 10.1016/j.ajhg.2013.02.003
*
Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner.
Stricker SH, Feber A, Engström PG, Carén H, Kurian KM, Takashima Y, Watts C, Way M, Dirks P, Bertone P, Smith A, Beck S, Pollard SM. Genes & development Volume 27 (2013) p.654-669 DOI: 10.1101/gad.212662.112
*
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.
Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C. Bioinformatics (Oxford, England) Volume 29 (2013) p.1112-1119 DOI: 10.1093/bioinformatics/btt096
*
Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC. Bioinformatics (Oxford, England) Volume 29 (2013) p.1343-1344 DOI: 10.1093/bioinformatics/btt106
The SHOCT domain: a widespread domain under-represented in model organisms.
Eberhardt RY, Bartholdson SJ, Punta M, Bateman A. PloS one Volume 8 (2013) p.e57848 DOI: 10.1371/journal.pone.0057848
*
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Nature genetics Volume 45 (2013) p.415-21, 421e1-2 DOI: 10.1038/ng.2568
BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC. Bioinformatics (Oxford, England) Volume 29 (2013) p.1103-1104 DOI: 10.1093/bioinformatics/btt100
*
A system-level, molecular evolutionary analysis of mammalian phototransduction.
Invergo BM, Montanucci L, Laayouni H, Bertranpetit J. BMC evolutionary biology Volume 13 (2013) p.52 DOI: 10.1186/1471-2148-13-52
*
In silico comparison of antimycobacterial natural products with known antituberculosis drugs.
Espinoza-Moraga M, Njuguna NM, Mugumbate G, Caballero J, Chibale K. Journal of chemical information and modeling Volume 53 (2013) p.649-660 DOI: 10.1021/ci300467b
*
Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data.
van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. PLoS computational biology Volume 9 (2013) p.e1002899 DOI: 10.1371/journal.pcbi.1002899
*
Genetic susceptibility to non-necrotizing erysipelas/cellulitis.
Hannula-Jouppi K, Massinen S, Siljander T, Mäkelä S, Kivinen K, Leinonen R, Jiao H, Aitos P, Karppelin M, Vuopio J, Syrjänen J, Kere J. PloS one Volume 8 (2013) p.e56225 DOI: 10.1371/journal.pone.0056225
*
Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Biochimica et biophysica acta Volume 1844 (2014) p.98-107 DOI: 10.1016/j.bbapap.2013.02.017
*
Crystal structure of the entire respiratory complex I.
Baradaran R, Berrisford JM, Minhas GS, Sazanov LA. Nature Volume 494 (2013) p.443-448 DOI: 10.1038/nature11871
*
Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.4009-4014 DOI: 10.1073/pnas.1219747110
*
Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.
Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M, Naghra H, Cotton JA, Berriman M, Britton C, Gilleard JS. International journal for parasitology Volume 43 (2013) p.465-475 DOI: 10.1016/j.ijpara.2012.12.011
*
Critical assessment of automated flow cytometry data analysis techniques.
Aghaeepour N, Finak G, FlowCAP Consortium, DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Nature methods Volume 10 (2013) p.228-238 DOI: 10.1038/nmeth.2365
The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat005 DOI: 10.1093/database/bat005
*
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
Anderson JW, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J. Bioinformatics (Oxford, England) Volume 29 (2013) p.704-710 DOI: 10.1093/bioinformatics/btt050
*
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.
Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E. Nucleic acids research Volume 41 (2013) p.3600-3618 DOI: 10.1093/nar/gkt030
*
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ. Genome biology Volume 14 (2013) p.R11 DOI: 10.1186/gb-2013-14-2-r11
*
PRIDE Cluster: building a consensus of proteomics data.
Griss J, Foster JM, Hermjakob H, Vizcaíno JA. Nature methods Volume 10 (2013) p.95-96 DOI: 10.1038/nmeth.2343
*
Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy.
Vita F, Lucarotti V, Alpi E, Balestrini R, Mello A, Bachi A, Alessio M, Alpi A. Proteome science Volume 11 (2013) p.7 DOI: 10.1186/1477-5956-11-7
A ligand's-eye view of protein similarity.
van Westen GJ, Overington JP. Nature methods Volume 10 (2013) p.116-117 DOI: 10.1038/nmeth.2339
*
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes.
Studer RA, Dessailly BH, Orengo CA. The Biochemical journal Volume 449 (2013) p.581-594 DOI: 10.1042/bj20121221
*
Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.
Nishi H, Fong JH, Chang C, Teichmann SA, Panchenko AR. Molecular bioSystems Volume 9 (2013) p.1620-1626 DOI: 10.1039/c3mb25514j
*
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.
Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V. Journal of proteomics Volume 87 (2013) p.134-138 DOI: 10.1016/j.jprot.2013.01.019
*
Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC. Genome biology Volume 14 (2013) p.R7 DOI: 10.1186/gb-2013-14-1-r7
*
The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.
Li MA, Pettitt SJ, Eckert S, Ning Z, Rice S, Cadiñanos J, Yusa K, Conte N, Bradley A. Molecular and cellular biology Volume 33 (2013) p.1317-1330 DOI: 10.1128/mcb.00670-12
*
Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Nature biotechnology Volume 31 (2013) p.126-134 DOI: 10.1038/nbt.2486
*
A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. Nature methods Volume 10 (2013) p.221-227 DOI: 10.1038/nmeth.2340
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Nature Volume 494 (2013) p.77-80 DOI: 10.1038/nature11875
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R. Database : the journal of biological databases and curation Volume 2013 (2013) p.bas062 DOI: 10.1093/database/bas062
CySBGN: a Cytoscape plug-in to integrate SBGN maps.
Gonçalves E, van Iersel M, Saez-Rodriguez J. BMC bioinformatics Volume 14 (2013) p.17 DOI: 10.1186/1471-2105-14-17
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ. Proteins Volume 81 (2013) p.583-591 DOI: 10.1002/prot.24213
UniChem: a unified chemical structure cross-referencing and identifier tracking system.
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP. Journal of cheminformatics Volume 5 (2013) p.3 DOI: 10.1186/1758-2946-5-3
*
Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene.
Hanning JE, Saini HK, Murray MJ, van Dongen S, Davis MP, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, Coleman N. British journal of cancer Volume 108 (2013) p.450-460 DOI: 10.1038/bjc.2012.564
*
Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.
LeishGEN Consortium, Wellcome Trust Case Control Consortium 2, Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, Donnelly P. Nature genetics Volume 45 (2013) p.208-213 DOI: 10.1038/ng.2518
*
Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.
Auburn S, Marfurt J, Maslen G, Campino S, Ruano Rubio V, Manske M, Machunter B, Kenangalem E, Noviyanti R, Trianty L, Sebayang B, Wirjanata G, Sriprawat K, Alcock D, Macinnis B, Miotto O, Clark TG, Russell B, Anstey NM, Nosten F, Kwiatkowski DP, Price RN. PloS one Volume 8 (2013) p.e53160 DOI: 10.1371/journal.pone.0053160
*
A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones.
Hirani N, Westenberg M, Gami MS, Davis P, Hope IA, Dolphin CT. BMC biotechnology Volume 13 (2013) p.1 DOI: 10.1186/1472-6750-13-1
*
Histone deacetylase 1 and 2 are essential for normal T-cell development and genomic stability in mice.
Dovey OM, Foster CT, Conte N, Edwards SA, Edwards JM, Singh R, Vassiliou G, Bradley A, Cowley SM. Blood Volume 121 (2013) p.1335-1344 DOI: 10.1182/blood-2012-07-441949
Building models using Reactome pathways as templates.
Croft D. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.273-283 DOI: 10.1007/978-1-62703-450-0_14
*
Diagnostic criteria and clinical guidelines standardization to automate case classification.
Courtot M, Zheng J, Stoeckert CJ, Brinkman RR, Ruttenberg A. CEURS proceedings: International Conference on Biomedical Ontologies Volume 1060 (2013) p.101-104
Supporting SBML as a model exchange format in software applications.
Keating SM, Le Novère N. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.201-225 DOI: 10.1007/978-1-62703-450-0_11
*
Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED, Teichmann S. Progress in molecular biology and translational science Volume 117 (2013) p.25-51 DOI: 10.1016/b978-0-12-386931-9.00002-7
*
Protein Data Resources
Furnham N, Garavelli JS, Thornton JM. Encyclopaedia of Biological Chemistry Academic Press (2nd Ed)
The Ramachandran plot and protein structure validation
Laskowski RA, Furnham N, Thornton JM. Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map World Scientific Publishing DOI: 10.1142/9789814449144_0005
*
Emdatabank: Unified Data Resource for 3DEM
Catherine Lawson, Ardan Patwardhan, Grigore D Pintilie, Eduardo Sanz Garcia, Ingvar Lagerstedt, Matthew L Baker, Raul Sala, Steven J Ludtke, Helen M Berman, Gerard Kleywegt, Wah Chiu. Biophysical journal Volume 104 (2013) p.351a DOI: 10.1016/j.bpj.2012.11.1950
*
Construction of cell type-specific logic models of signaling networks using CellNOpt.
Morris MK, Melas I, Saez-Rodriguez J. Methods in molecular biology (Clifton, N.J.) Volume 930 (2013) p.179-214 DOI: 10.1007/978-1-62703-059-5_8
Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.
Fonseca NA, Morales-Hojas R, Reis M, Rocha H, Vieira CP, Nolte V, Schlötterer C, Vieira J. Genome biology and evolution Volume 5 (2013) p.661-679 DOI: 10.1093/gbe/evt037
Bioinformatics workflows and web services in systems biology made easy for experimentalists.
Jimenez RC, Corpas M. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.299-310 DOI: 10.1007/978-1-62703-450-0_16
Modeling signaling networks with different formalisms: a preview.
MacNamara A, Henriques D, Saez-Rodriguez J. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.89-105 DOI: 10.1007/978-1-62703-450-0_5
*
T-cell activation induces selective changes of cellular lipidome.
Lonnberg T, Yetukuri L, Seppanen-Laakso T, Lahesmaa R, Oresic M. Frontiers in bioscience (Elite edition) Volume 5 (2013) p.558-573 DOI: 10.2741/e638
*
The Ramachandran Plot and Protein Structure Validation
Laskowski RA, Furnham N, Thornton JM. Biomolecular Forms and Functions, A Celebration of 50 years of the Ramachandran Map World Scientific Publishing
Controlled annotations for systems biology.
Juty N, Laibe C, Le Novère N. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.227-245 DOI: 10.1007/978-1-62703-450-0_12
BioModels Database: a repository of mathematical models of biological processes.
Chelliah V, Laibe C, Le Novère N. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.189-199 DOI: 10.1007/978-1-62703-450-0_10
*
The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2013) p.456-458
*
Maximising proteomics data for the scientific community
Hermjakob H, Apweiler R. European Pharmaceutical Review Volume 9 (2013) p.23-29
Proteomics data exchange and storage: the need for common standards and public repositories.
Jiménez RC, Vizcaíno JA. Methods in molecular biology (Clifton, N.J.) Volume 1007 (2013) p.317-333 DOI: 10.1007/978-1-62703-392-3_14
*
The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.
Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T. Genome biology Volume 14 (2013) p.R98 DOI: 10.1186/gb-2013-14-9-r98
Visualization and analysis of biological networks.
Millán PP. Methods in molecular biology (Clifton, N.J.) Volume 1021 (2013) p.63-88 DOI: 10.1007/978-1-62703-450-0_4