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
Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression.
Gordon K, Clouaire T, Bao XX, Kemp SE, Xenophontos M, de Las Heras JI, Stancheva I. Nucleic acids research Volume 42 (2014) p.3529-3541 DOI: 10.1093/nar/gkt1351
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
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
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
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
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
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
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
DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S. Genomics Volume 103 (2014) p.1-10 DOI: 10.1016/j.ygeno.2013.11.005
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Echidna venom gland transcriptome provides insights into the evolution of monotreme venom.
Wong ES, Nicol S, Warren WC, Belov K. PloS one Volume 8 (2013) p.e79092 DOI: 10.1371/journal.pone.0079092
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
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, 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
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
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
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
Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
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
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
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
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
Allele-specific regulation of DISC1 expression by miR-135b-5p.
Rossi M, Kilpinen H, Muona M, Surakka I, Ingle C, Lahtinen J, Hennah W, Ripatti S, Hovatta I. European journal of human genetics : EJHG Volume 22 (2014) p.840-843 DOI: 10.1038/ejhg.2013.246
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
Novel anti-plasmodial hits identified by virtual screening of the ZINC database.
Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC. Journal of computer-aided molecular design Volume 27 (2013) p.859-871 DOI: 10.1007/s10822-013-9685-z
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
The Drosophila anatomy ontology.
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. Journal of biomedical semantics Volume 4 (2013) p.32 DOI: 10.1186/2041-1480-4-32
The Drosophila phenotype ontology.
Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV. Journal of biomedical semantics Volume 4 (2013) p.30 DOI: 10.1186/2041-1480-4-30
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
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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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The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
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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
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Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.
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Synthesis and in vitro and in vivo pharmacological evaluation of new 4-aminoquinoline-based compounds.
Tukulula M, Njoroge M, Abay ET, Mugumbate GC, Wiesner L, Taylor D, Gibhard L, Norman J, Swart KJ, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Kameni-Tcheudji J, Chibale K. ACS medicinal chemistry letters Volume 4 (2013) p.1198-1202 DOI: 10.1021/ml400311r
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
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Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
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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
Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
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Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
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ISCB computational biology Wikipedia competition.
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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
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Transcriptome and genome sequencing uncovers functional variation in humans.
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Monitoring named entity recognition: the League Table.
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OntoQuery: easy-to-use web-based OWL querying.
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Exploiting disjointness axioms to improve semantic similarity measures.
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Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
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Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
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The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.
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How community has shaped the Protein Data Bank.
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Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
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The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.
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Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
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The COMBREX project: design, methodology, and initial results.
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Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
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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
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
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.
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Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.
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The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
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SMIM1 underlies the Vel blood group and influences red blood cell traits.
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A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
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Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.
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A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
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Ensembl: Filmed browser workshop
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Maximising proteomics data for the scientific community
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Expression Atlas: Quick tour
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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
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
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
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The future of genome-based medicine.
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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
Building models using Reactome pathways as templates.
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Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.
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Ensembl: Filmed API Workshop
Perry E. DOI: 10.6019/tol.ensapi-v.2013.00001.1
The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.
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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
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
Protein Data Resources
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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
Molecular fields in ligand discovery.
Gane PJ, Chan AW. Methods in molecular biology (Clifton, N.J.) Volume 1008 (2013) p.479-499 DOI: 10.1007/978-1-62703-398-5_18
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
Europe PMC: Quick tour
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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