Biography:Amos Bairoch

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Amos Bairoch
SIB Bairoch.jpg
Amos Bairoch
Born (1957-11-22) 22 November 1957 (age 66)[1]
Alma materUniversity of Geneva[2]
Known for
Awards
  • Proteomics pioneer award (2013)[1]
  • Otto Naegeli prize (2010)
  • European Latsis Prize (2004)
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[2][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

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.[citation needed]

Research

His main work[5] 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[5] 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

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

References

  1. ↑ 1.0 1.1 1.2 1.3 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. ↑ 2.0 2.1 "Amos Bairoch's home page". ExPASy. Archived from the original on 2014-02-14. https://web.archive.org/web/20140214004338/http://web.expasy.org/groups/people/amos.html. 
  3. ↑ 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. PMID 2041811. 
  4. ↑ 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. PMID 12824418. 
  5. ↑ 5.0 5.1 5.2 Amos Bairoch publications indexed by Google Scholar
  6. ↑ 6.0 6.1 Amos Bairoch's publications indexed by the Scopus bibliographic database. (Subscription content?)
  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 2013-12-06. https://web.archive.org/web/20131406505900/http://www.isb-sib.ch/groups/geneva/calipho-bairoch.html. 
  9. ↑ "SIB's Bairoch to Step Down as Swiss-Prot Director to Launch New Human Protein Resource". GenomeWeb.com. Archived from the original on 2012-02-20. https://web.archive.org/web/20120220003341/http://www.genomeweb.com/informatics/sibs-bairoch-step-down-swiss-prot-director-launch-new-human-protein-resource. 
  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. 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. 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. 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. 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. 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. 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. 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. PMID 8594586. 
  19. ↑ Bairoch, A (1994). "The ENZYME data bank". Nucleic Acids Research 22 (17): 3626–7. doi:10.1093/nar/22.17.3626. PMID 7937072. 
  20. ↑ Bairoch, A (1993). "The ENZYME data bank". Nucleic Acids Research 21 (13): 3155–6. doi:10.1093/nar/21.13.3155. PMID 8332535. 
  21. ↑ Bairoch, A. (1991). "SEQANALREF: A sequence analysis bibliographic reference databank". Computer Applications in the Biosciences (CABIOS) 7 (2): 268. doi:10.1093/bioinformatics/7.2.268. PMID 2059856. http://doc.rero.ch/record/300192/files/7-2-268.pdf. 
  22. ↑ 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. PMID 2041810. 
  23. ↑ 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. 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. Archived from the original on 2011-02-11. https://web.archive.org/web/20110211051808/http://www.genomeweb.com/no-new-deals-geneprot-close-its-doors. 
  27. ↑ Lane, L; Argoud-Puy, G; Britan, A; Cusin, I; Duek, P. D.; Evalet, O; Gateau, A; Gaudet, P et al. (2012). "Ne Xt Prot: A knowledge platform for human proteins". Nucleic Acids Research 40 (Database issue): D76-83. doi:10.1093/nar/gkr1179. PMID 22139911. 
  28. ↑ Gaudet, P; Michel, P. A.; Zahn-Zabal, M; Cusin, I; Duek, P. D.; Evalet, O; Gateau, A; Gleizes, A et al. (2015). "The neXtProt' knowledgebase on human proteins: Current status". Nucleic Acids Research 43 (Database issue): D764-70. doi:10.1093/nar/gku1178. PMID 25593349. 
  29. ↑ Gaudet, P; Argoud-Puy, G; Cusin, I; Duek, P; Evalet, O; Gateau, A; Gleizes, A; Pereira, M et al. (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. et al. (2004). "The Universal Protein Resource (UniProt)". Nucleic Acids Research 33 (Database issue): D154–D159. doi:10.1093/nar/gki070. PMID 15608167. 
  31. ↑ Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K. et al. (2003). "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003". Nucleic Acids Research 31 (1): 365–370. doi:10.1093/nar/gkg095. PMID 12520024. 
  32. ↑ Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L. et al. (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. PMID 11125043. 
  33. ↑ Mulder, N. J.; Apweiler, R; Attwood, T. K.; Bairoch, A; Barrell, D; Bateman, A; Binns, D; Biswas, M et al. (2003). "The InterPro Database, 2003 brings increased coverage and new features". Nucleic Acids Research 31 (1): 315–8. doi:10.1093/nar/gkg046. PMID 12520011. 
  34. ↑ Mulder, N. J. (2005). "InterPro, progress and status in 2005". Nucleic Acids Research 33 (Database issue): D201-5. doi:10.1093/nar/gki106. PMID 15608177.  open access
  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. 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. 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. doi:10.1038/387394a0. PMID 9163424. 
  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. https://archive-ouverte.unige.ch/unige:40347/ATTACHMENT01. 
  39. ↑ Gaudet, P. (2011). "Towards BioDBcore: A community-defined information specification for biological databases". Database 2011: baq027. doi:10.1093/database/baq027. PMID 21205783. 
  40. ↑ "HUPO Distinguished Awards". HUPO. Archived from the original on 2013-06-05. https://web.archive.org/web/20130605151023/http://www.hupo.org/communications/HUPO_awards/. 
  41. ↑ Waldrop, M. (2008). "Big data: Wikiomics". Nature 455 (7209): 22–5. doi:10.1038/455022a. PMID 18769412. 




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