Amos Bairoch

Amos Bairoch

Amos Bairoch
Born November 22, 1957 (1957-11-22) (age 54)
Fields Bioinformatics
Institutions Swiss Institute of Bioinformatics
Alma mater University of Geneva[1]
Doctoral students Alexandre Gattiker
Pavel Dobrokhotov
Fabrice David[1]
Known for Swiss-Prot[2], ExPASy[3]
Notable awards European Latsis Prize (2004), Otto Naegeli prize (2010)

Amos Bairoch is a Swiss bioinformatician, born 22 November 1957[4].

Bairoch is currently professor of Bioinformatics at the Department of Structural biology and Bioinformatics of the University of Geneva and group leader at the Swiss Institute of Bioinformatics (SIB). He has created at the SIB a new group called CALIPHO (Computer Analysis and Laboratory Investigation of Proteins of Human Origin)[5] to combine bioinformatics, curation, and experimental efforts to functionally characterize human proteins [6].

His main work[7][8] is in the field of protein sequence analysis and more particularly in the development of databases and software tools for this purpose. His most important contribution is the input of human knowledge by careful manual annotation in protein-related data.[9] His first project, as a Ph.D. student was the development of PC/Gene[10], an MS-DOS based software package for the analysis of protein and nucleotide sequences. PC/Gene was commercialized, first by a Swiss company (Genofit) then by Intelligenetics in the US which was later bought by Oxford Molecular.

While working on PC/Gene he started to develop an annotated protein sequence database which became Swiss-Prot and was first released in July 1986.[11] From 1988 onward it has been a collaborative project with the Data Library group of the European Molecular Biology Laboratory which later evolved into the European Bioinformatics Institute (EBI).

The Swiss-Prot database is the primary protein sequence resource in the world and has been a key research instrument for both bioinformaticians and laboratory-based scientists in a very wide range of applications.[12] A measure of its success is the recent development of UniProt, the world’s most comprehensive catalogue of information on proteins.[13] UniProt is a central information resource of protein sequences and functions created by joining the information contained in Swiss-Prot, TrEMBL, and the American Protein Information Resource databases.

In 1988 he started to develop PROSITE[14], a database of protein families and domains. A little while later he created ENZYME, a nomenclature database on enzymes as well as SeqAnalRef[15], a sequence analysis bibliographic reference database,.[16][17]

In collaboration with Ron Appel he initiated, in August 1993, the first molecular biology WWW server, ExPASy[18]. What was intended as a prototype grew rapidly into a major site that provides access to the many databases produced partially or completely in Geneva as well as many tools for the analysis of proteins (proteomics).

In 1998, with colleagues in Geneva and Lausanne, he was one of the founders of the Swiss Institute of Bioinformatics (SIB), whose mission is to establish in Switzerland a center of excellence in the field of bioinformatics with an emphasis on research, education, services and the developments of databases and tools.[19]

In November 1997, together with Ron Appel and Denis Hochstrasser, he founded GeneBio (Geneva Bioinformatics SA), a company involved in biological knowledge. In April 2000, the above persons with Keith Rose and Robin Offord founded GeneProt (Geneva Proteomics), a high throughput proteomics company that ceased operations in 2005.

Since 2009, in the framework of the CALIPHO group, directed by himself and Lydie Lane, he is involved in the development of neXtProt a new resource which aim to provide life scientists with a broad spectrum of knowledge on all human proteins.

He is recipient of the 1993 Friedrich Miescher Award from the Swiss Society of Biochemistry, the 1995 Helmut Horten Foundation Incentive Award, the 2004 Pehr Edman award, the 2004 European Latsis Prize, the 2010 Otto Naegeli prize, and the 2011 HUPO Distinguished Achievement Award in Proteomic Sciences[1].

Quotes

“ As the process keeps going down we're reaching the point where every genome that can be sequenced will be sequenced.[20] ”

References

  1. ^ a b http://www.expasy.ch/people/personal/amos/amos_cv.html Amos Bairoch CV
  2. ^ Bairoch, A.; Boeckmann, B. (1991). "The SWISS-PROT protein sequence data bank". Nucleic Acids Research 19 Suppl: 2247–2249. doi:10.1093/nar/19.suppl.2247. PMC 331359. PMID 2041811. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=331359.  edit
  3. ^ Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A. (2003). "ExPASy: The proteomics server for in-depth protein knowledge and analysis". Nucleic Acids Research 31 (13): 3784–3788. doi:10.1093/nar/gkg563. PMC 168970. PMID 12824418. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168970.  edit
  4. ^ http://www.expasy.ch/people/amos.html Amos Bairoch's home page on the ExPASy website
  5. ^ http://www.isb-sib.ch/groups/geneva/calipho-bairoch.html CALIPHO's page on the SIB website
  6. ^ http://www.genomeweb.com/informatics/sibs-bairoch-step-down-swiss-prot-director-launch-new-human-protein-resource
  7. ^ http://scholar.google.com/scholar?q=amos+bairoch Amos Bairoch publications in Google Scholar
  8. ^ http://www.biomedexperts.com/Profile.bme/70784/Amos_Bairoch Amos Bairoch profile in BiomedExperts
  9. ^ Lima, T.; Auchincloss, A. H.; Coudert, E.; Keller, G.; Michoud, K.; Rivoire, C.; Bulliard, V.; De Castro, E. et al. (2009). "HAMAP: A database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot". Nucleic Acids Research 37 (Database issue): D471–D478. doi:10.1093/nar/gkn661. PMC 2686602. PMID 18849571. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2686602.  edit
  10. ^ Moore, J.; Engelberg, A.; Bairoch, A. (1988). "Using PC/GENE for protein and nucleic acid analysis". BioTechniques 6 (6): 566–572. PMID 3273189.  edit
  11. ^ Bairoch, A. (2000). "Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!". Bioinformatics 16 (1): 48–64. doi:10.1093/bioinformatics/16.1.48. PMID 10812477.  edit — a historical account by Bairoch.
  12. ^ Persson, B. (2000). "Bioinformatics in protein analysis". EXS 88: 215–231. PMID 10803381.  edit
  13. ^ Wu, C. H.; Apweiler, R.; Bairoch, A.; Natale, D. A.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E. et al. (2006). "The Universal Protein Resource (UniProt): An expanding universe of protein information". Nucleic Acids Research 34 (90001): D187–D191. doi:10.1093/nar/gkj161. PMC 1347523. PMID 16381842. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347523.  edit
  14. ^ Hofmann, K.; Bucher, P.; Falquet, L.; Bairoch, A. (1999). "The PROSITE database, its status in 1999". Nucleic Acids Research 27 (1): 215–219. doi:10.1093/nar/27.1.215. PMC 148139. PMID 9847184. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=148139.  edit
  15. ^ Bairoch, A. (1991). "SEQANALREF: A sequence analysis bibliographic reference databank". Computer applications in the biosciences : CABIOS 7 (2): 268. PMID 2059856.  edit
  16. ^ Bairoch, A. (1991). "PROSITE: A dictionary of sites and patterns in proteins". Nucleic Acids Research 19 Suppl: 2241–2245. doi:10.1093/nar/19.suppl.2241. PMC 331358. PMID 2041810. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=331358.  edit
  17. ^ Hulo, N.; Bairoch, A.; Bulliard, V.; Cerutti, L.; Cuche, B. A.; De Castro, E.; Lachaize, C.; Langendijk-Genevaux, P. S. et al. (2007). "The 20 years of PROSITE". Nucleic Acids Research 36 (Database issue): D245–D249. doi:10.1093/nar/gkm977. PMC 2238851. PMID 18003654. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2238851.  edit
  18. ^ Appel, R. D.; Bairoch, A.; Hochstrasser, D. F. (1994). "A new generation of information retrieval tools for biologists: The example of the ExPASy WWW server". Trends in biochemical sciences 19 (6): 258–260. doi:10.1016/0968-0004(94)90153-8. PMID 8073505.  edit
  19. ^ Hoogland, C.; Mostaguir, K.; Appel, R.; Lisacek, F. (2008). "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server". Journal of Proteomics 71 (2): 245–248. doi:10.1016/j.jprot.2008.02.005. PMID 18617148.  edit
  20. ^ Waldrop, M. (2008). "Big data: Wikiomics". Nature 455 (7209): 22. doi:10.1038/455022a. PMID 18769412.  edit