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Rolf Apweiler

Joint Associate Director of EMBL-EBI

E-mail: apweiler@ebi.ac.uki

EMBL Outstation European Bioinformatics Institute (EMBL/EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom
Phone: +44 (0)1223 494435
Fax: +44 (0)1223 494468

Short biography

Dr. Rolf Apweiler has a PhD in Biochemistry from the Zentrum fuer Molekulare Biologie Heidelberg (ZMBH) and the University of Heidelberg, and is an EMBL Senior Scientist. Dr. Apweiler has been working on the Swiss-Prot protein sequence database since 1987, and in 1994 he became leader of the Swiss-Prot group at the EMBL Outstation European Bioinformatics Institute (EMBL-EBI) in Cambridge. Later he has been leading the Sequence Database Group at EMBL-EBI, and 2007-2012 he was Joint Head of the Protein and Nucleotide Data (PANDA) Group, together with Ewan Birney. The group is actively involved in many international collaborations and initiatives like the Human Proteome Organization (HUPO) Proteomics Standards Initiative (HPSI), which was chaired by Dr. Apweiler 2002-2005. In 2012, he was made Joint Associate Director of EMBL-EBI, and together with Ewan Birney has strategic oversight of all EMBL-EBI services. He is a member of several more committees, review panels and advisory boards, including the Nomenclature Committee of IUBMB (the “Enzyme Commission”), the FlyBase advisory board, the Scientific Committee of the Helmholtz Centre for Infection Research (HZI), and the Scientific Advisory Board of the Human Proteome Resource (HPR) program in Sweden. Dr. Apweiler is also editor of the FEBS Journal, Section Editor of BMC Bioinformatics, and serves on several more editorial or advisory boards of other scientific journals. He has published 240 papers and book chapters and is a frequent invited speaker for lectures and tutorials at universities, companies, and conferences. Dr. Apweiler is involved in a number of national and international collaborations with industry and academic research organisations, and his work is supported by national and international funding agencies.

Group

The Protein and Nucleotide Database Group (PANDA) provides all the sequence resources at EMBL-EBI, from DNA through to Protein and encompassing the associated databases, such as genome databases (e.g. Ensembl), protein families (e.g. InterPro), protein function (e.g. UniProt), proteomics (e.g. IntAct), ontologies (e.g. GO), and pathways (e.g. Reactome). The manually annotated data resources are complemented by well-evaluated automated systems to provide optimum coverage of knowledge space. Also, locally installable database and analysis systems for complex data types are developed, like UniProt-DAS and PRIDE. The PANDA group is jointly headed by Dr. Rolf Apweiler and Dr. Ewan Birney. The philosophy of the PANDA team is to capture, organise and interpret sequence-related data, providing all information freely to all groups in a variety of formats, including user friendly web sites. Wherever possible, we aim to collaborate with other groups worldwide with similar aims.

Selected publications

  1. O’Donovan C, Apweiler R : A guide to UniProt for protein scientists. Methods Mol. Biol. 694: 25-35 (2011).
  2. UniProt Consortium: Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39: D214-9 (2011).
  3. Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K: A large-scale protein-function database. Nat. Chem. Biol. 6: 785 (2010).
  4. The Gene Ontology Consortium: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38: D331-5 (2010).
  5. Binns D., Dimmer E, Huntley R, Barrell D, O’Donovan C, Apweiler R: Quickgo: A Web-Based Tool for Gene Ontology Searching. Bioinformatics 25: 3045-6 (2009).
  6. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C: InterPro: the integrative protein signature database. Nucleic Acids Res. 37: D211-5 (2009).
  7. Ilsley GR, Luscombe NM, Apweiler R: Know Your Limits: Assumptions, Constraints and Interpretation in Systems Biology. Biochimica et Biophysica Acta 1794: 1280-7 (2009).
  8. 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, Martin-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: Prepublication data sharing. Nature 461: 168-70 (2009).
  9. Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox A, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 36: D5-12 (2008).
  10. Jungblut PR, Holzhutter HG, Apweiler R, Schluter H: The speciation of the proteome. Chemistry Central Journal 2: 16 (2008).
  11. Mulder N.J., Kersey P., Pruess M., Apweiler R.: In silico characterization of proteins: UniProt, InterPro and Integr8. Mol. Biotechnol. 38: 165-177 (2008).
  12. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novere N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol. 26: 889-96 (2008).
  13. Cote RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H: The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 8: 401 (2007).
  14. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H: IntAct – open source resource for molecular interaction data. Nucleic Acids Res. 35: D561-5 (2007).
  15. Martens L, Orchard S, Apweiler R, Hermjakob H: Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy. Mol. Cell Proteomics 6: 1666-7 (2007).