Publications for 2009

2009

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From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium. Cellular and molecular life sciences : CMLS Volume 67 (2010) p.1049-1064 DOI: 10.1007/s00018-009-0229-6
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Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009.
Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J. Standards in genomic sciences Volume 1 (2009) p.278-282 DOI: 10.4056/sigs.641096
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E. PloS one Volume 4 (2009) p.e8407 DOI: 10.1371/journal.pone.0008407
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A small-cell lung cancer genome with complex signatures of tobacco exposure.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordoñez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ. Nature Volume 463 (2010) p.184-190 DOI: 10.1038/nature08629
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Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Genome research Volume 20 (2010) p.180-189 DOI: 10.1101/gr.099226.109
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Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. PLoS computational biology Volume 5 (2009) p.e1000585 DOI: 10.1371/journal.pcbi.1000585
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Bioclipse 2: a scriptable integration platform for the life sciences.
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE. BMC bioinformatics Volume 10 (2009) p.397 DOI: 10.1186/1471-2105-10-397
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Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H. Nucleic acids research Volume 38 (2010) p.D870-1 DOI: 10.1093/nar/gkp1078
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
Cochrane GR, Galperin MY. Nucleic acids research Volume 38 (2010) p.D1-4 DOI: 10.1093/nar/gkp1077
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Recurated protein interaction datasets.
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H. Nature methods Volume 6 (2009) p.860-861 DOI: 10.1038/nmeth1209-860
BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Li C, Courtot M, Le Novère N, Laibe C. Briefings in bioinformatics Volume 11 (2010) p.270-277 DOI: 10.1093/bib/bbp056
The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J. Nucleic acids research Volume 38 (2010) p.D17-25 DOI: 10.1093/nar/gkp986
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The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium. Nucleic acids research Volume 38 (2010) p.D331-5 DOI: 10.1093/nar/gkp1018
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Finding query suggestions for PubMed.
Lu Z, Wilbur WJ, McEntyre JR, Iskhakov A, Szilagyi L. AMIA ... Annual Symposium proceedings. AMIA Symposium Volume 2009 (2009) p.396-400
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Comparative ecophysiology and genomics of the toxic unicellular alga Fibrocapsa japonica.
Guidi-Rontani C, Maheswari U, Jabbari K, Bowler C. The New phytologist Volume 185 (2010) p.446-458 DOI: 10.1111/j.1469-8137.2009.03074.x
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WormBase: a comprehensive resource for nematode research.
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW. Nucleic acids research Volume 38 (2010) p.D463-7 DOI: 10.1093/nar/gkp952
Gene expression atlas at the European bioinformatics institute.
Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A. Nucleic acids research Volume 38 (2010) p.D690-8 DOI: 10.1093/nar/gkp936
Ensembl's 10th year.
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM. Nucleic acids research Volume 38 (2010) p.D557-62 DOI: 10.1093/nar/gkp972
The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L. Nucleic acids research Volume 38 (2010) p.D736-42 DOI: 10.1093/nar/gkp964
Improvements to services at the European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G. Nucleic acids research Volume 38 (2010) p.D39-45 DOI: 10.1093/nar/gkp998
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The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L, Toribio AL, Parkhill J, Dougan G, Frankel G, Thomson NR. Journal of bacteriology Volume 192 (2010) p.525-538 DOI: 10.1128/jb.01144-09
ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E. Comptes rendus biologies Volume 332 (2009) p.1050-1058 DOI: 10.1016/j.crvi.2009.09.003
Non-redundant patent sequence databases with value-added annotations at two levels.
Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R. Nucleic acids research Volume 38 (2010) p.D52-6 DOI: 10.1093/nar/gkp960
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FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B. Nucleic Acids Research Volume 38 (2010) p.D443-7 DOI: 10.1093/nar/gkp910
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. Proteomics Volume 9 (2009) p.5112-5119 DOI: 10.1002/pmic.200900189
Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E. Nature methods Volume 6 (2009) p.S6-S12 DOI: 10.1038/nmeth.1376
Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A. Nucleic acids research Volume 38 (2010) p.D563-9 DOI: 10.1093/nar/gkp871
PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. Nucleic Acids Research Volume 38 (2010) p.D308-17 DOI: 10.1093/nar/gkp916
Chemical Entities of Biological Interest: an update.
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C. Nucleic acids research Volume 38 (2010) p.D249-54 DOI: 10.1093/nar/gkp886
The IntAct molecular interaction database in 2010.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H. Nucleic acids research Volume 38 (2010) p.D525-31 DOI: 10.1093/nar/gkp878
OrChem - An open source chemistry search engine for Oracle(R).
Rijnbeek M, Steinbeck C. Journal of cheminformatics Volume 1 (2009) p.17 DOI: 10.1186/1758-2946-1-17
The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium. Nucleic acids research Volume 38 (2010) p.D142-8 DOI: 10.1093/nar/gkp846
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Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L. Drug discovery today Volume 15 (2010) p.3-15 DOI: 10.1016/j.drudis.2009.09.011
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Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray.
Samolski I, de Luis A, Vizcaíno JA, Monte E, Suárez MB. BMC microbiology Volume 9 (2009) p.217 DOI: 10.1186/1471-2180-9-217
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A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C. Nature genetics Volume 41 (2009) p.1182-1190 DOI: 10.1038/ng.467
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Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T. Genome biology Volume 10 (2009) p.R108 DOI: 10.1186/gb-2009-10-10-r108
Second Joint HUPO publication and Proteomics Standards Initiative workshop.
Orchard S, Binz PA, Hermjakob H. Proteomics Volume 9 (2009) p.4426-4428 DOI: 10.1002/pmic.200900406
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Network visualization and analysis of gene expression data using BioLayout Express(3D).
Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Nature protocols Volume 4 (2009) p.1535-1550 DOI: 10.1038/nprot.2009.177
Approaching clinical proteomics: current state and future fields of application in cellular proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G. Cytometry. Part A : the journal of the International Society for Analytical Cytology Volume 75 (2009) p.816-832 DOI: 10.1002/cyto.a.20779
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Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ. Science (New York, N.Y.) Volume 326 (2009) p.140-144 DOI: 10.1126/science.1177221
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Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I. Journal of chemical information and modeling Volume 49 (2009) p.2272-2289 DOI: 10.1021/ci900196u
Annual spring meeting of the Proteomics Standards Initiative.
Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H. Proteomics Volume 9 (2009) p.4429-4432 DOI: 10.1002/pmic.200900407
QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R. Database : the journal of biological databases and curation Volume 2009 (2009) p.bap010 DOI: 10.1093/database/bap010
EMMA--mouse mutant resources for the international scientific community.
Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D. Nucleic acids research Volume 38 (2010) p.D570-6 DOI: 10.1093/nar/gkp799
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Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis.
Zúñiga A, Hödar C, Hanna P, Ibáñez F, Moreno P, Pulgar R, Pastenes L, González M, Cambiazo V. BMC biology Volume 7 (2009) p.61 DOI: 10.1186/1741-7007-7-61
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PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M. Bioinformatics Volume 25 (2009) p.3183-3184 DOI: 10.1093/bioinformatics/btp545
QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. Bioinformatics (Oxford, England) Volume 25 (2009) p.3045-3046 DOI: 10.1093/bioinformatics/btp536
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Finding one's way in proteomics: a protein species nomenclature.
Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR. Chemistry Central journal Volume 3 (2009) p.11 DOI: 10.1186/1752-153x-3-11
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
Manakov SA, Grant SG, Enright AJ. BMC genomics Volume 10 (2009) p.419 DOI: 10.1186/1471-2164-10-419
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Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J. Nature Volume 461 (2009) p.168-170 DOI: 10.1038/461168a
A guide to the Proteomics Identifications Database proteomics data repository.
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L. Proteomics Volume 9 (2009) p.4276-4283 DOI: 10.1002/pmic.200900402
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In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N. Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.E95; author reply E96 DOI: 10.1073/pnas.0904550106
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The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RA, Bähler J. PLoS genetics Volume 5 (2009) p.e1000626 DOI: 10.1371/journal.pgen.1000626
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A method for visualizing CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF. Bioinformatics (Oxford, England) Volume 25 (2009) p.3012-3019 DOI: 10.1093/bioinformatics/btp495
A community standard format for the representation of protein affinity reagents.
Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. Molecular & cellular proteomics : MCP Volume 9 (2010) p.1-10 DOI: 10.1074/mcp.m900185-mcp200
Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM. Journal of cheminformatics Volume 1 (2009) p.12 DOI: 10.1186/1758-2946-1-12
The Systems Biology Graphical Notation.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. Nature biotechnology Volume 27 (2009) p.735-741 DOI: 10.1038/nbt.1558
Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM. Nature chemical biology Volume 5 (2009) p.521-525 DOI: 10.1038/nchembio0809-521
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Drug target central.
Harland L, Gaulton A. Expert opinion on drug discovery Volume 4 (2009) p.857-872 DOI: 10.1517/17460440903049290
The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ. Biochemical Society transactions Volume 37 (2009) p.723-726 DOI: 10.1042/bst0370723
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The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C. Structure (London, England : 1993) Volume 17 (2009) p.1051-1062 DOI: 10.1016/j.str.2009.06.015
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Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C. Proteomics Volume 9 (2009) p.3928-3933 DOI: 10.1002/pmic.200900247
A System for Information Management in BioMedical Studies--SIMBioMS.
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A. Bioinformatics (Oxford, England) Volume 25 (2009) p.2768-2769 DOI: 10.1093/bioinformatics/btp420
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Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W. Nature protocols Volume 4 (2009) p.1184-1191 DOI: 10.1038/nprot.2009.97
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM. PLoS computational biology Volume 5 (2009) p.e1000440 DOI: 10.1371/journal.pcbi.1000440
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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Reference Genome Group of the Gene Ontology Consortium. PLoS computational biology Volume 5 (2009) p.e1000431 DOI: 10.1371/journal.pcbi.1000431
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PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L. Nature biotechnology Volume 27 (2009) p.598-599 DOI: 10.1038/nbt0709-598
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Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics Volume 9 (2009) p.3626-3629 DOI: 10.1002/pmic.200900205
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Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R. Journal of proteome research Volume 8 (2009) p.3689-3692 DOI: 10.1021/pr900023z
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Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting.
Orchard S. Journal of proteome research Volume 8 (2009) p.3219 DOI: 10.1021/pr900527r
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Biophysical annotation and representation of CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF. Bioinformatics (Oxford, England) Volume 25 (2009) p.2263-2270 DOI: 10.1093/bioinformatics/btp391
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Bioinformatics (Oxford, England) Volume 25 (2009) p.2865-2871 DOI: 10.1093/bioinformatics/btp394
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A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ. BMC bioinformatics Volume 10 Suppl 6 (2009) p.S13 DOI: 10.1186/1471-2105-10-s6-s13
Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. Bioinformatics (Oxford, England) Volume 25 (2009) p.2092-2094 DOI: 10.1093/bioinformatics/btp354
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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. Genome research Volume 19 (2009) p.1316-1323 DOI: 10.1101/gr.080531.108
Evolution. Uniting alignments and trees.
Löytynoja A, Goldman N. Science (New York, N.Y.) Volume 324 (2009) p.1528-1529 DOI: 10.1126/science.1175949
Protein Evolution – Sequence, Structure and Systems
Sternberg M, Thornton J, Laskowski R. The Biochemist Biochemical Society
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Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S. Bioinformatics (Oxford, England) Volume 25 (2009) p.i145-53 DOI: 10.1093/bioinformatics/btp215
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A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group. Nature methods Volume 6 (2009) p.423-430 DOI: 10.1038/nmeth.1333
*
Genome watch: What a scorcher!
Cerdeño-Tárraga AM. Nature reviews. Microbiology Volume 7 (2009) p.408-409 DOI: 10.1038/nrmicro2154
Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A. TheScientificWorldJournal Volume 9 (2009) p.420-423 DOI: 10.1100/tsw.2009.57
*
DNA methylation-histone modification relationships across the desmin locus in human primary cells.
Lindahl Allen M, Koch CM, Clelland GK, Dunham I, Antoniou M. BMC molecular biology Volume 10 (2009) p.51 DOI: 10.1186/1471-2199-10-51
Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM. Journal of molecular biology Volume 390 (2009) p.560-577 DOI: 10.1016/j.jmb.2009.05.015
*
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR. Genome biology Volume 10 (2009) p.R51 DOI: 10.1186/gb-2009-10-5-r51
Know your limits: assumptions, constraints and interpretation in systems biology.
Ilsley GR, Luscombe NM, Apweiler R. Biochimica et biophysica acta Volume 1794 (2009) p.1280-1287 DOI: 10.1016/j.bbapap.2009.05.002
*
Infrastructure for the life sciences: design and implementation of the UniProt website.
Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E. BMC bioinformatics Volume 10 (2009) p.136 DOI: 10.1186/1471-2105-10-136
*
A protein interaction network for the large conductance Ca(2+)-activated K(+) channel in the mouse cochlea.
Kathiresan T, Harvey M, Orchard S, Sakai Y, Sokolowski B. Molecular & cellular proteomics : MCP Volume 8 (2009) p.1972-1987 DOI: 10.1074/mcp.m800495-mcp200
*
Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified.
Mehta A, Orchard S. Molecular and cellular biochemistry Volume 329 (2009) p.3-15 DOI: 10.1007/s11010-009-0114-5
*
CellML metadata standards, associated tools and repositories.
Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Volume 367 (2009) p.1845-1867 DOI: 10.1098/rsta.2008.0310
*
Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.
Pink CJ, Swaminathan SK, Dunham I, Rogers J, Ward A, Hurst LD. Genome biology and evolution Volume 1 (2009) p.13-22 DOI: 10.1093/gbe/evp001
Applications of high-throughput sequencing to chromatin structure and function in mammals.
Dunham I. F1000 biology reports Volume 1 (2009) p.32 DOI: 10.3410/b1-32
*
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.
Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D. Genome research Volume 19 (2009) p.994-1005 DOI: 10.1101/gr.089086.108
*
Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Bioinformatics (Oxford, England) Volume 25 (2009) p.2088-2089 DOI: 10.1093/bioinformatics/btp256
*
An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.
Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP. Nature genetics Volume 41 (2009) p.614-618 DOI: 10.1038/ng.369
*
Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.
Motallebipour M, Enroth S, Punga T, Ameur A, Koch C, Dunham I, Komorowski J, Ericsson J, Wadelius C. The FEBS journal Volume 276 (2009) p.1878-1890 DOI: 10.1111/j.1742-4658.2009.06914.x
*
Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets.
Blanco L, Mead JA, Bessant C. Journal of proteome research Volume 8 (2009) p.1782-1791 DOI: 10.1021/pr800792z
*
Planning the human variome project: the Spain report.
Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS, Contributors to the Human Variome Project Planning Meeting. Human mutation Volume 30 (2009) p.496-510 DOI: 10.1002/humu.20972
Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.
Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J. Journal of chemical theory and computation Volume 5 (2009) p.982-992 DOI: 10.1021/ct800508v
*
The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients.
Holden MTG, Seth-Smith HMB, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EPC, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J. Journal of bacteriology Volume 191 (2009) p.2907-2907
The need for speed.
Flicek P. Genome Biology Volume 10 (2009) p.212 DOI: 10.1186/gb-2009-10-3-212
The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM. FEBS letters Volume 583 (2009) p.1692-1698 DOI: 10.1016/j.febslet.2009.03.019
*
Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Journal of molecular biology Volume 388 (2009) p.356-380 DOI: 10.1016/j.jmb.2009.02.052
WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM. Bioinformatics Volume 25 (2009) p.1192-1194 DOI: 10.1093/bioinformatics/btp116
*
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Genes & development Volume 23 (2009) p.619-632 DOI: 10.1101/gad.1760209
*
Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.
Carlile M, Swan D, Jackson K, Preston-Fayers K, Ballester B, Flicek P, Werner A. Nucleic acids research Volume 37 (2009) p.2274-2282 DOI: 10.1093/nar/gkp088
*
A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC. Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.3829-3834 DOI: 10.1073/pnas.0808382106
*
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase Consortium, Aebersold R, Hafen E. BMC bioinformatics Volume 10 (2009) p.59 DOI: 10.1186/1471-2105-10-59
*
Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network. Genome biology Volume 10 (2009) p.401 DOI: 10.1186/gb-2009-10-2-401
Correction: Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Genome biology Volume 10 (2009) p.402-402
*
Protein function annotation by homology-based inference.
Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A. Genome biology Volume 10 (2009) p.207 DOI: 10.1186/gb-2009-10-2-207
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.
Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA. Proteomics Volume 9 (2009) p.499-501 DOI: 10.1002/pmic.200800838
*
Recent developments in public proteomic MS repositories and pipelines.
Mead JA, Bianco L, Bessant C. Proteomics Volume 9 (2009) p.861-881 DOI: 10.1002/pmic.200800553
HUPO World Congress Publication Committee meeting. August 2008, Amsterdam, The Netherlands.
Orchard S, Ping P. Proteomics Volume 9 (2009) p.502-503 DOI: 10.1002/pmic.200800839
Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM. Journal of the Royal Society, Interface Volume 6 (2009) p.129-147 DOI: 10.1098/rsif.2008.0341
*
Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM. Nature biotechnology Volume 27 (2009) p.157-167 DOI: 10.1038/nbt1519
*
Integrating sequence, evolution and functional genomics in regulatory genomics.
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E. Genome biology Volume 10 (2009) p.202 DOI: 10.1186/gb-2009-10-1-202
*
Case-controlled structure validation.
Read RJ, Kleywegt GJ. Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.140-147 DOI: 10.1107/s0907444908041085
*
On vital aid: the why, what and how of validation.
Kleywegt GJ. Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.134-139 DOI: 10.1107/s090744490900081x
*
Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF. Experimental physiology Volume 94 (2009) p.472-485 DOI: 10.1113/expphysiol.2008.045161
*
Systematic comparison of the human saliva and plasma proteomes.
Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT. Proteomics. Clinical applications Volume 3 (2009) p.116-134 DOI: 10.1002/prca.200800140
Approaching clinical proteomics: current state and future fields of application in fluid proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Clinical chemistry and laboratory medicine Volume 47 (2009) p.724-744 DOI: 10.1515/cclm.2009.167
*
In silico identification of genes in bacteriophage DNA.
Kropinski AM, Borodovsky M, Carver TJ, Cerdeño-Tárraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS. Methods in molecular biology (Clifton, N.J.) Volume 502 (2009) p.57-89 DOI: 10.1007/978-1-60327-565-1_6
*
A framework for annotating and visualizing cellML models.
Wimalaratne SM.
Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson JD, Thornton JM. From Molecules to Medicines: Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism Springer Netherlands DOI: 10.1007/978-90-481-2339-1_13
Integrated Servers for Structure-Informed Function Prediction
Laskowski RA. From Protein Structure to Function with Bioinformatics Springer Netherlands DOI: 10.1007/978-1-4020-9058-5_10
*
Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C. Proteomics Volume 9 (2009) p.218-222 DOI: 10.1002/pmic.200800732
Algorithms and databases.
Martens L, Apweiler R. Methods in molecular biology (Clifton, N.J.) Volume 564 (2009) p.245-259 DOI: 10.1007/978-1-60761-157-8_14
*
Verification of Uncurated Protein Annotations.
Couto F, Silva V, Lee E, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D. Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration Global Publishing
Visualising the Epigenome
Flicek P, Birney E. Epigenomics Springer Netherlands DOI: 10.1007/978-1-4020-9187-2_4
New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J. Chemistry Central journal Volume 3 (2009) p.O3 DOI: 10.1186/1752-153x-3-s1-o3