Papers
2011
• Aranda B, Blankenburg H, Kerrien S, Brinkman FSL, Ceol A, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interaction Nature Methods, 2011 Jun 29;8(7):528-529. doi: 10.1038/nmeth.1637
• Alcantara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C. Rhea - a manually curated resource of biochemical reactions Nucl. Acids Res., 2011 doi: 10.1093/nar/gkr1126
• Burmester A, Shelest E, Glöckner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh V, Hertweck C, Hube B, White TC, Platzer M, Guthke R, Heitman J, Wöstemeyer J, Zipfel PF, Monod M, Brakhage AA. Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi Genome Biol. 2011 Jan 19;12(1):R7. Epub 2011 Jan 19 doi: 10.1186/gb-2011-12-1-r7
• Cochrane G, Karsch-Mizrachi I, Nakamura Y, on behalf of the International Nucleotide Sequence Database Collaboration (2011) The International Nucleotide Sequence Database Collaboration Nucleic Acids Res. 39 (Suppl 1): D15-18 doi: 10.1093/nar/gkq1150>/i>
• Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Singh Riat H, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Y. Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez1 XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011 Nucl. Acids Res. (2011) 39 (suppl 1): D800-D806. doi: 10.1093/nar/gkq1064
• Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment Bioinformatics (2011) 27 (6): 867-869. doi: 10.1093/bioinformatics/btr012
• Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D. The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources Nucl. Acids Res. (2011) 39 (suppl 1):D507-D513. doi: 10.1093/nar/gkq968
• Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M. The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web PLoS ONE 6(10): e25513 (2011) doi: 10.1371/journal.pone.0025513
• Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments Nucleic Acids Res. 2011 Nov 7. doi: 10.1093/nar/gkr913 [Epub ahead of print]
• Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V and Cochrane G. (2011) The European Nucleotide Archive Nucleic Acids Res. 39 (Suppl 1): D28-31 doi: 10.1093/nar/gkq967
• Leinonen R, Sugawara H and Shumway M, on behalf of the International Nucleotide Sequence Database Collaboration (2011) The Sequence Read Archive Nucl. Acids Res. 39 (Suppl 1): D19-21 doi: 10.1093/nar/gkq1019
• Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A. UniPathway: a resource for the exploration and annotation of metabolic pathways Nucleic Acids Res. 2011 doi: 10.1093/nar/gkr1023 [Epub ahead of print]
• Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments Nucleic Acids Res.(2011) Jan;39(Database issue):D1002-4 doi: 10.1093/nar/gkq1040
• Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011 Nucl. Acids Res. (2011) 39 (suppl 1):D670-D676. doi: 10.1093/nar/gkq1089
• Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CWG, Jacob J, Fernandes P, Nyronen T, De Las Rivas J, Blicher T, Loveland J, McDowall J, Jones P, Vaughan B, Lopez R, Attwood TK, Brooksbank C. Bioinformatics Training Network (BTN): A community resource for bioinformatics trainers Brief Bioinform (2011), first published online: November 22, 2011. doi: 10.1093/bib/bbr064
• Söhngen C, Chang A, Schomburg D. Development of a classification scheme for disease-related enzyme information BMC Bioinformatics (Aug 2011) 12:329 (PubMed ID 21827651) doi:10.1186/1471-2105-12-329
• The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2011 doi: 10.1093/nar/gkr981 [Epub ahead of print]
• The UniProt Consortium. Ongoing and future developments at the Universal Protein Resource Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. Epub 2010 Nov 4. doi: 10.1093/nar/gkq1020
• Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JAM, Tramontano A, Schneider MV. Ten simple rules for developing a short bioinformatics training course PLoS Computational Biology: Editorial, published 27 Oct 2011. doi: 10.1371/journal.pcbi.1002245
• Wang R, et al. PRIDE Inspector: a tool to visualize and validate MS proteomics data Nat Biotechnol. 2011 [In press]
2010
• Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments Nucl. Acids Res. (2010) 39(suppl 1): D1002-D1004. doi: 10.1093/nar/gkq1040
• Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert Jr CJ, Ball C. Annotare - a tool for annotating high-throughput biomedical investigations and resultant data Bioinformatics (2010) 26 (19): 2470-2471. doi: 10.1093/bioinformatics/btq462
• Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C. Bioinformatics training: a review of challenges, actions and support requirements Brief Bioinform. 2010 Nov;11(6):544-51. doi: 10.1093/bib/bbq021