Amos Bairoch

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Amos Bairoch
SIB Bairoch.jpg
Amos Bairoch
Born (1957-11-22) 22 November 1957 (age 65) [1]
Alma mater University of Geneva [2]
Known for
Awards
Scientific career
Fields
Institutions Swiss Institute of Bioinformatics
Website web.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]

Contents

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

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

Related Research Articles

<span class="mw-page-title-main">Post-translational modification</span> Biological processes

Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process often occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.

<span class="mw-page-title-main">UniProt</span> Database of protein sequences and functional information

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.

The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases

The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them.

<span class="mw-page-title-main">PROSITE</span> Database of protein domains, families and functional sites

PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation. PROSITE was created in 1988 by Amos Bairoch, who directed the group for more than 20 years. Since July 2018, the director of PROSITE and Swiss-Prot is Alan Bridge.

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.

SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal transduction, and a single protein may play a role in multiple processes or cellular pathways.

neXtProt is an on-line knowledge platform on human proteins. It strives to be a comprehensive resource that provides a variety of types of information on human proteins, such as their function, subcellular location, expression, interactions and role in diseases. The major part of the information in neXtProt is obtained from the UniProt Swiss-Prot database but it is complemented by data originating from high-throughput studies with an emphasis on proteomics. neXtProt offers also an advanced search capacity based on the SPARQL technology as well as an API that allows to programatically extract the data stored in the resource. It is developed by the CALIPHO group directed by Amos Bairoch and Lydie Lane of the Swiss Institute of Bioinformatics (SIB).

OMPdb is a dedicated database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria. Such proteins are responsible for a broad range of important functions, like passive nutrient uptake, active transport of large molecules, protein secretion, as well as adhesion to host cells, through which bacteria expose their virulence activity.

<span class="mw-page-title-main">Rolf Apweiler</span>

Rolf Apweiler is a director of European Bioinformatics Institute (EBI) part of the European Molecular Biology Laboratory (EMBL) with Ewan Birney.

SWISS-MODEL is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology modelling methods make use of experimental protein structures ("templates") to build models for evolutionary related proteins ("targets").

<span class="mw-page-title-main">Terri Attwood</span> British bioinformatics researcher

Teresa K. Attwood is a Professor of Bioinformatics in the Department of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI). She held a Royal Society University Research Fellowship at University College London (UCL) from 1993 to 1999 and at the University of Manchester from 1999 to 2002.

In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.

Julian John Thurstan Gough is a Group Leader in the Laboratory of Molecular Biology (LMB) of the Medical Research Council (MRC). He was previously a professor of bioinformatics at the University of Bristol.

<span class="mw-page-title-main">Christine Orengo</span> Professor of Bioinformatics

Christine Anne Orengo is a Professor of Bioinformatics at University College London (UCL) known for her work on protein structure, particularly the CATH database. Orengo serves as president of the International Society for Computational Biology (ISCB), the first woman to do so in the history of the society.

In molecular biology, MvirDB is a publicly available database that stores information on toxins, virulence factors and antibiotic resistance genes. Sources that this database uses for DNA and protein information include: Tox-Prot, SCORPION, the PRINTS Virulence Factors, VFDB, TVFac, Islander, ARGO and VIDA. The database provides a BLAST tool that allows the user to query their sequence against all DNA and protein sequences in MvirDB. Information on virulence factors can be obtained from the usage of the provided browser tool. Once the browser tool is used, the results are returned as a readable table that is organized by ascending E-Values, each of which are hyperlinked to their related page. MvirDB is implemented in an Oracle 10g relational database.

References

  1. 1 2 3 4 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. 1 2 "Amos Bairoch's home page". ExPASy. Archived from the original on 14 February 2014.
  3. ↑ 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.
  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. PMC   168970 . PMID   12824418.
  5. 1 2 3 Amos Bairoch publications indexed by Google Scholar
  6. 1 2 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 XtProt: 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 XtProt: 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 logo PLoS transparent.svg
  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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