Publications for 2013


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Evolution of the thermopsin peptidase family (A5).
Rawlings ND. PloS one Volume 8 (2013) p.e78998 DOI: 10.1371/journal.pone.0078998
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
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
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
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
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
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
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
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
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
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
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
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
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
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
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Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
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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
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
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
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
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
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
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
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
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
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
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
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
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
Journal of the American Chemical Society Volume 135 (2013) p.10178 DOI: 10.1021/ja403136h
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
LifeTrain: towards a European framework for continuing professional development in biomedical sciences
Brooksbank C. Nature reviews. Drug discovery (2013) DOI: 10.1038/nrd4026
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
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
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) DOI: 10.1093/database/bat040
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
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
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/
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
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
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
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
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
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
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
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
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
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
World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA.
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Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
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Construction of cell type-specific logic models of signaling networks using CellNOpt.
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Bioinformatics workflows and web services in systems biology made easy for experimentalists.
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Supporting SBML as a model exchange format in software applications.
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Proteomics data exchange and storage: the need for common standards and public repositories.
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Emdatabank: Unified Data Resource for 3DEM
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