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Papers | sling-fp7.org

Papers

2012

• Flicek P, et al. Ensembl 2012 Nucl. Acids Res. (2012) 40(D1): D84-D90 doi: http://dx.doi.org/10.1093/nar/gkr991

• Jungo F, Bougueleret L, Xenariosa I, Poux S. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data Toxicon Volume 60, Issue 4, 15 September 2012, Pages 551–557
doi: http://dx.doi.org/10.1016/j.toxicon.2012.03.010

• 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. (2012) 40 (D1): D1077-D1081
doi: http://dx.doi.org/10.1093/nar/gkr913

• Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H. The IntAct molecular interaction database in 2012 Nucl. Acids Res. (2012) 40 (D1): D841-D846 doi: http://dx.doi.org/10.1093/nar/gkr1088

• Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DST, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species Nucl. Acids Res. (2012) 40 (D1): D91-D97 doi: http://dx.doi.org/10.1093/nar/gkr895

• Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching Bioinformatics (2012) 28 (12): 1650-1651
doi: http://dx.doi.org/10.1093/bioinformatics/bts240

• Pedersen CNS, Axelsen KB, Harper JF, Palmgren MG. Evolution of Plant P-Type ATPases Front Plant Sci. 2012; 3: 31. Published online 2012 February 21 http://dx.doi.org/doi:10.3389/fpls.2012.00031

• Wang R, Fabregat A, Rios D, Ovelleiro D, Foster JM, Cote RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaino JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data Nature Biotechnology 30:135–137 (2012) doi: http://dx.doi.org/10.1038/nbt.2112

• Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA. Improvements in the protein identifier cross-reference service Nucl. Acids Res. (2012) 40 (W1): W276-W280 doi: http://dx.doi.org/10.1093/nar/gks338

• Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H. MageComet--web application for harmonizing existing large-scale experiment descriptions Bioinformatics (2012) 28 (10): 1402-1403
doi: http://dx.doi.org/10.1093/bioinformatics/bts148

2011

• Adamusiak T, Burdett T, Kurbatova N, van der Velde KJ, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA. OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript BMC Bioinformatics 2011, 12:218 doi: http://dx.doi.org/10.1186/1471-2105-12-218

• 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. (2012) 40 (D1): D754-D760 doi: http://dx.doi.org/10.1093/nar/gkr1126

• 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: http://dx.doi.org/10.1038/nmeth.1637

• 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: http://dx.doi.org/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: http://dx.doi.org/10.1093/nar/gkq1150

• 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: http://dx.doi.org/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: http://dx.doi.org/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: http://dx.doi.org/10.1093/nar/gkq968

• Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA. Published and perished? The influence of the searched protein database on the long-term storage of proteomics data Mol Cell Proteomics. 2011 September; 10(9): M111.008490.
doi: http://dx.doi.org/10.1074/mcp.M111.008490

• 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: http://dx.doi.org/10.1371/journal.pone.0025513

• Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space Database (Oxford) 2011 Published online 2011 July 23 doi: http://dx.doi.org/10.1093/database/bar030

• Lang M, Stelzer M, Schomburg D. BKM-react, an integrated biochemical reaction database BMC Biochemistry 2011, 12:42 (2011) doi: http://dx.doi.org/10.1186/1471-2091-12-42

• 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: http://dx.doi.org/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: http://dx.doi.org/10.1093/nar/gkq1019

• Magrane M, The UniProt Consortium. UniProt Knowledgebase: a hub of integrated protein data Database: The Journal of Biological Databases and Curation (2011) doi: http://dx.doi.org/10.1093/database/bar009

• 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: http://dx.doi.org/10.1093/nar/gkr1023

• 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: http://dx.doi.org/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: http://dx.doi.org/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: http://dx.doi.org/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: http://dx.doi.org/10.1186/1471-2105-12-329

• Sriranganadane D, Waridel P, Salamin K, Feuermann M, Mignon B, Staib P, Neuhaus J-M, Quadroni M, Monod M. Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH Proteomics
Volume 11, Issue 22, pages 4422–4433, No. 22 November 2011
doi: http://dx.doi.org/10.1002/pmic.201100234

• The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucl. Acids Res. (2012) 40 (D1): D71-D75 doi: http://dx.doi.org/10.1093/nar/gkr981

• 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: http://dx.doi.org/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: http://dx.doi.org/10.1371/journal.pcbi.1002245

2010

• Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H. The Ontology Lookup Service: bigger and better Nucl. Acids Res. (2010) 38 (suppl 2): W155-W160 doi: http://dx.doi.org/10.1093/nar/gkq331

• Flicek P, et al. Ensembl’s 10th year Nucl. Acids Res. (2010) 38 (suppl 1): D557-D562 doi: http://dx.doi.org/10.1093/nar/gkp972

• Hinz U, The UniProt Consortium. From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase Cellular and Molecular Life Sciences Volume 67, Number 7 (2010), 1049-1064
doi: http://dx.doi.org/10.1007/s00018-009-0229-6

• Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I. Animal Toxins: How is Complexity Represented in Databases? Toxins 2010, 2(2), 262-282 doi: http://dx.doi.org/10.3390/toxins2020261

• Schneider V, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter M-C, 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) 11 (6): 544-551 doi: http://dx.doi.org/10.1093/bib/bbq021

• Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert Jr CJ, Ball CA. Annotare—a tool for annotating high-throughput biomedical investigations and resulting data Bioinformatics (2010) 26 (19): 2470-2471 doi: http://dx.doi.org/10.1093/bioinformatics/btq462

2009

• Adams N, de Matos P, Dekker A, Ennis M, Hastings J, Haug K, Hull D, Josephs Z, Moreno P, Turner S, Steinbeck C. Semantic access to chemistry data with the ChEBI ontology and web services CEUR Workshop Proceedings: Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS-2009), Amsterdam, The Netherlands, November 20, 2009

• Barsnes H, Vizcaíno JA, Eidhammer I, Martens L. PRIDE Converter: making proteomics data-sharing easy Nature Biotechnology 27, 598 - 599 (2009) doi: http://dx.doi.org/10.1038/nbt0709-598

• de Matos PM, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C. Chemical Entities of Biological Interest: an update Nucl. Acids Res. (Oct 2009) doi: http://dx.doi.org/10.1093/nar/gkp886

• Hastings J, de Matos P, Ennis M, Steinbeck C. Towards automatic classification within the ChEBI ontology Nature Precedings (2009) doi: http://dx.doi.org/10.1038/npre.2009.3525.1

• Hubbard TJP, et al. Ensembl 2009 Nucl. Acids Res. (2009) 37 (suppl 1): D690-D697
doi: http://dx.doi.org/10.1093/nar/gkn828