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Amos Bairoch

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"Bairoch" redirects here. For the economic historian, see Paul Bairoch.

Amos Bairoch
Amos Bairoch
Born (1957-11-22) 22 November 1957 (age 66)[1]
Alma materUniversity of Geneva[3]
Known for
Awards
Scientific career
Fields
InstitutionsSwiss Institute of Bioinformatics
Websiteweb.expasy.org/groups/people/amos.html

Amos Bairoch (born 22 November 1957)[1] is a Swiss bioinformatician[3][6][7] and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group[8] at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.[9]

His father was the economic historian Paul Bairoch.

Education

[edit]

His first project as a PhD 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.[citation needed]

Research

[edit]

His main work[2] 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.[11]

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.[12] 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.[13] A measure of its success is the recent development of UniProt, the world's most comprehensive catalogue of information on proteins.[14] 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 (PIR) databases.

In 1988, he started to develop PROSITE,[15] a database of protein families and domains. A little while later he created ENZYME,[16][17][18][19][20] a nomenclature database on enzymes as well as SeqAnalRef,[21] a sequence analysis bibliographic reference database.[22][23]

In collaboration with Ron Appel he initiated, in August 1993, the first molecular biology WWW server, ExPASy.[24] 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 SIB Swiss Institute of Bioinformatics, 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.[25]

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.[26]

Since 2009, in the framework of the CALIPHO group, directed by himself and Lydie Lane, he is involved in the development of neXtProt[27][28][29] a resource which aims to provide life scientists with a broad spectrum of knowledge on all human proteins.

He is also involved in the development of the Cellosaurus a knowledge resource on cell lines.

According to Google Scholar[2] and Scopus,[6] As of 2015 his most highly cited peer reviewed papers in scientific journals have been published in Nucleic Acids Research,[30][31][32][33][34] the Biochemical Journal,[35][36] Nature,[37] Briefings in Bioinformatics,[38] and Database.[39]

Awards and honours

[edit]

Bairoch was the 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, the 2011 HUPO Distinguished Achievement Award in Proteomic Sciences.,[40] the 2013 EUPA proteomics pioneer award,[1] and in 2018 the ABRF Award.

Quotes

[edit]

As the process keeps going down we're reaching the point where every genome that can be sequenced will be sequenced.[41]

References

[edit]
  1. ^ a b c d Lisacek, F.; Lane, L. (2014). "Proteomics Pioneer Award 2013: Professor Amos Bairoch, University of Geneva, Switzerland". EuPA Open Proteomics. 2: 34. doi:10.1016/j.euprot.2013.12.002.
  2. ^ a b c Amos Bairoch publications indexed by Google Scholar
  3. ^ a b "Amos Bairoch's home page". ExPASy. Archived from the original on 14 February 2014.
  4. ^ Bairoch, A.; Boeckmann, B. (1991). "The SWISS-PROT protein sequence data bank". Nucleic Acids Research. 19 Suppl (Suppl): 2247–2249. doi:10.1093/nar/19.suppl.2247. PMC 331359. PMID 2041811.
  5. ^ 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.
  6. ^ a b Amos Bairoch's publications indexed by the Scopus bibliographic database. (subscription required)
  7. ^ Amos Bairoch publications from Europe PubMed Central
  8. ^ "CALIPHO (Computer Analysis and Laboratory Investigation of Proteins of Human Origin) group page on the SIB website". Archived from the original on 20 April 2013.
  9. ^ "SIB's Bairoch to Step Down as Swiss-Prot Director to Launch New Human Protein Resource". GenomeWeb.com. Archived from the original on 20 February 2012.
  10. ^ Moore, J.; Engelberg, A.; Bairoch, A. (1988). "Using PC/GENE for protein and nucleic acid analysis". BioTechniques. 6 (6): 566–572. PMID 3273189.
  11. ^ Lima, T.; Auchincloss, A. H.; Coudert, E.; Keller, G.; Michoud, K.; Rivoire, C.; Bulliard, V.; De Castro, E.; Lachaize, C.; Baratin, D.; Phan, I.; Bougueleret, L.; Bairoch, A. (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.
  12. ^ 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. – a historical account by Bairoch.
  13. ^ Persson, B. (2000). "Bioinformatics in protein analysis". EXS. 88: 215–231. doi:10.1007/978-3-0348-8458-7_14. ISBN 978-3-0348-9576-7. PMID 10803381.
  14. ^ Wu, C. H.; Apweiler, R.; Bairoch, A.; Natale, D. A.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Mazumder, R.; O'Donovan, C.; Redaschi, N.; Suzek, B. (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.
  15. ^ 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.
  16. ^ Bairoch, A (2000). "The ENZYME database in 2000". Nucleic Acids Research. 28 (1): 304–5. doi:10.1093/nar/28.1.304. PMC 102465. PMID 10592255.
  17. ^ Bairoch, A (1999). "The ENZYME data bank in 1999". Nucleic Acids Research. 27 (1): 310–1. doi:10.1093/nar/27.1.310. PMC 148167. PMID 9847212.
  18. ^ Bairoch, A (1996). "The ENZYME data bank in 1995". Nucleic Acids Research. 24 (1): 221–2. doi:10.1093/nar/24.1.221. PMC 145615. PMID 8594586.
  19. ^ Bairoch, A (1994). "The ENZYME data bank". Nucleic Acids Research. 22 (17): 3626–7. doi:10.1093/nar/22.17.3626. PMC 308334. PMID 7937072.
  20. ^ Bairoch, A (1993). "The ENZYME data bank". Nucleic Acids Research. 21 (13): 3155–6. doi:10.1093/nar/21.13.3155. PMC 309744. PMID 8332535.
  21. ^ Bairoch, A. (1991). "SEQANALREF: A sequence analysis bibliographic reference databank" (PDF). Computer Applications in the Biosciences. 7 (2): 268. doi:10.1093/bioinformatics/7.2.268. PMID 2059856.
  22. ^ Bairoch, A. (1991). "PROSITE: A dictionary of sites and patterns in proteins". Nucleic Acids Research. 19 Suppl (Suppl): 2241–2245. doi:10.1093/nar/19.suppl.2241. PMC 331358. PMID 2041810.
  23. ^ Hulo, N.; Bairoch, A.; Bulliard, V.; Cerutti, L.; Cuche, B. A.; De Castro, E.; Lachaize, C.; Langendijk-Genevaux, P. S.; Sigrist, C. J. A. (2007). "The 20 years of PROSITE". Nucleic Acids Research. 36 (Database issue): D245–D249. doi:10.1093/nar/gkm977. PMC 2238851. PMID 18003654.
  24. ^ 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.
  25. ^ 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.
  26. ^ "With No New Deals, GeneProt to Close Its Doors". GenomeWeb.com. June 2005. Archived from the original on 11 February 2011.
  27. ^ Lane, L; Argoud-Puy, G; Britan, A; Cusin, I; Duek, P. D.; Evalet, O; Gateau, A; Gaudet, P; Gleizes, A; Masselot, A; Zwahlen, C; Bairoch, A (2012). "Ne Xt Prot: A knowledge platform for human proteins". Nucleic Acids Research. 40 (Database issue): D76-83. doi:10.1093/nar/gkr1179. PMC 3245017. PMID 22139911.
  28. ^ Gaudet, P; Michel, P. A.; Zahn-Zabal, M; Cusin, I; Duek, P. D.; Evalet, O; Gateau, A; Gleizes, A; Pereira, M; Teixeira, D; Zhang, Y; Lane, L; Bairoch, A (2015). "The neXtProt' knowledgebase on human proteins: Current status". Nucleic Acids Research. 43 (Database issue): D764-70. doi:10.1093/nar/gku1178. PMC 4383972. PMID 25593349.
  29. ^ Gaudet, P; Argoud-Puy, G; Cusin, I; Duek, P; Evalet, O; Gateau, A; Gleizes, A; Pereira, M; Zahn-Zabal, M; Zwahlen, C; Bairoch, A; Lane, L (2013). "Ne Xt Prot: Organizing protein knowledge in the context of human proteome projects". Journal of Proteome Research. 12 (1): 293–8. doi:10.1021/pr300830v. PMID 23205526.
  30. ^ Bairoch, A.; Apweiler, R.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O'Donovan, C.; Redaschi, N.; Yeh, L. S. (2004). "The Universal Protein Resource (UniProt)". Nucleic Acids Research. 33 (Database issue): D154–D159. doi:10.1093/nar/gki070. PMC 540024. PMID 15608167.
  31. ^ Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M. (2003). "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003". Nucleic Acids Research. 31 (1): 365–370. doi:10.1093/nar/gkg095. PMC 165542. PMID 12520024.
  32. ^ Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L.; Corpet, F.; Croning, M. D.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Hermjakob, H.; Hulo, N.; Jonassen, I.; Kahn, D.; Kanapin, A.; Karavidopoulou, Y.; Lopez, R.; Marx, B.; Mulder, N. J.; Oinn, T. M.; Pagni, M.; Servant, F.; Sigrist, C. J.; Zdobnov, E. M. (2001). "The InterPro database, an integrated documentation resource for protein families, domains and functional sites". Nucleic Acids Research. 29 (1): 37–40. doi:10.1093/nar/29.1.37. PMC 29841. PMID 11125043.
  33. ^ Mulder, N. J.; Apweiler, R; Attwood, T. K.; Bairoch, A; Barrell, D; Bateman, A; Binns, D; Biswas, M; Bradley, P; Bork, P; Bucher, P; Copley, R. R.; Courcelle, E; Das, U; Durbin, R; Falquet, L; Fleischmann, W; Griffiths-Jones, S; Haft, D; Harte, N; Hulo, N; Kahn, D; Kanapin, A; Krestyaninova, M; Lopez, R; Letunic, I; Lonsdale, D; Silventoinen, V.; Orchard, S. E.; Pagni, M.; Pagni, Marco; Peyruc, D.; Ponting, C.P.; Selengut, J.D.; Servant, F.; Sigrist, C.J.A.; Vaughan, R.; Zdobnov, E.M. (2003). "The InterPro Database, 2003 brings increased coverage and new features". Nucleic Acids Research. 31 (1): 315–8. doi:10.1093/nar/gkg046. PMC 165493. PMID 12520011.
  34. ^ Mulder, N. J.; Apweiler, R; Attwood, T. K.; Bairoch, A; Bateman, A; Binns, D; Bradley, P; Bork, P; Bucher, P; Cerutti, L; Copley, R; Courcelle, E; Das, U; Durbin, R; Fleischmann, W; Gough, J; Haft, D; Harte, N; Hulo, N; Kahn, D; Kanapin, A; Krestyaninova, M; Lonsdale, D; Lopez, R; Letunic, I; Madera, M; Maslen, J; McDowall, J; Mitchell, A; et al. (2005). "InterPro, progress and status in 2005". Nucleic Acids Research. 33 (Database issue): D201-5. doi:10.1093/nar/gki106. PMC 540060. PMID 15608177. Open access icon
  35. ^ Henrissat, B; Bairoch, A (1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 (2): 695–6. doi:10.1042/bj3160695. PMC 1217404. PMID 8687420.
  36. ^ Henrissat, B; Bairoch, A (1993). "New families in the classification of glycosyl hydrolases based on amino acid sequence similarities". The Biochemical Journal. 293 (3): 781–8. doi:10.1042/bj2930781. PMC 1134435. PMID 8352747.
  37. ^ Freiberg, C.; Fellay, R. M.; Bairoch, A.; Broughton, W. J.; Rosenthal, A.; Perret, X. (1997). "Molecular basis of symbiosis between Rhizobium and legumes". Nature. 387 (6631): 394–401. Bibcode:1997Natur.387..394F. doi:10.1038/387394a0. PMID 9163424. S2CID 4336941.
  38. ^ Sigrist, C. J.; Cerutti, L; Hulo, N; Gattiker, A; Falquet, L; Pagni, M; Bairoch, A; Bucher, P (2002). "PROSITE: A documented database using patterns and profiles as motif descriptors". Briefings in Bioinformatics. 3 (3): 265–74. doi:10.1093/bib/3.3.265. PMID 12230035.
  39. ^ Gaudet, P.; Bairoch, A.; Field, D.; Sansone, S. -A.; Taylor, C.; Attwood, T. K.; Bateman, A.; Blake, J. A.; Bult, C. J.; Cherry, J. M.; Chisholm, R. L.; Cochrane, G.; Cook, C. E.; Eppig, J. T.; Galperin, M. Y.; Gentleman, R.; Goble, C. A.; Gojobori, T.; Hancock, J. M.; Howe, D. G.; Imanishi, T.; Kelso, J.; Landsman, D.; Lewis, S. E.; Karsch Mizrachi, I.; Orchard, S.; Ouellette, B. F. F.; Ranganathan, S.; Richardson, L.; Rocca-Serra, P. (2011). "Towards BioDBcore: A community-defined information specification for biological databases". Database. 2011: baq027. doi:10.1093/database/baq027. PMC 3017395. PMID 21205783.
  40. ^ "HUPO Distinguished Awards". HUPO. Archived from the original on 5 June 2013.
  41. ^ Waldrop, M. (2008). "Big data: Wikiomics". Nature. 455 (7209): 22–5. doi:10.1038/455022a. PMID 18769412.
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