Alex Bateman

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Alex Bateman
Alex Bateman ISMBECCB 2013.jpg
Alex Bateman speaking at the Intelligent Systems for Molecular Biology (ISMB) conference in Berlin in 2013
Born Alexander George Bateman
(1972-10-09) October 9, 1972 (age 45)[1]
Alma mater
Known for
Awards
Scientific career
Fields
Institutions
Thesis Evolution of the structure and function of the immunoglobulin superfamily (1997)
Doctoral advisor Cyrus Chothia
Other academic advisors Richard M. Durbin[10]
Website www.ebi.ac.uk/about/people/alex-bateman

Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK.[9][11] He has led the development of the Pfam biological database[12] and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.[13][14][15][16][17]

Education[edit]

Bateman received a Bachelor of Science degree in Biochemistry from Newcastle University in 1994. He received his PhD from the University of Cambridge in 1997, for research supervised by Cyrus Chothia[18][19] on the evolution of the immunoglobulin protein superfamily.[20][21] During this time, he also worked with Sean Eddy to discover novel protein domains using the HMMER software.[22]

Career and research[edit]

In 1997, Bateman joined the Wellcome Trust Sanger Institute to lead the development of the Pfam biological database. In 2003, he introduced the Rfam database of RNA families.[6][22] He was also involved in providing protein analysis for the publication of the human genome.[22][23]

As of 2012, he has been Head of Protein Sequence Resources at EMBL-EBI.[24]

Bateman has also been involved in promoting the use of Wikipedia within the science community[25] and in particular, community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through WikiProject RNA.[26]

Bateman served as Executive Editor of the journal Bioinformatics from 2004 to 2012 and has also served as Editor of Nucleic Acids Research, Genome Biology and Current Protocols in Bioinformatics.[2][3] In 2014, he was appointed one of the first Honorary Editors of Bioinformatics.[27] As of 2015, Bateman also serves on the ISCB Board of Directors.[28]

Awards and honours[edit]

Bateman was awarded the 2010 Benjamin Franklin Award in bioinformatics.[29][30] He became the third former member of Richard Durbin's lab to win the award, following Sean Eddy and Ewan Birney.[29][10] Bateman was elected an ISCB Fellow in 2017 by the International Society for Computational Biology.[8][31]

Alex Bateman (left) and Cyrus Chothia (right), at the ISMB conference in Dublin in 2015

References[edit]

  1. ^ Alex Bateman at Library of Congress Authorities
  2. ^ a b "Alex Bateman: Senior Team Leader Protein Sequence Resources and Group Leader Bateman Research Group". Uniprot.org. Archived from the original on 2015-03-16. 
  3. ^ a b "Alex Bateman Publons". Publons.com. Archived from the original on 2015-03-16. 
  4. ^ Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L.; Studholme, D. J.; Yeats, C.; Eddy, S. R. (2004). "The Pfam protein families database". Nucleic Acids Research. 32 (Database issue): 138D–1141. doi:10.1093/nar/gkh121. ISSN 0305-1048. PMC 308855Freely accessible. PMID 14681378.  open access publication – free to read
  5. ^ Sammut, S. J.; Finn, R. D.; Bateman, A (2008). "Pfam 10 years on: 10,000 families and still growing". Briefings in Bioinformatics. 9 (3): 210–9. doi:10.1093/bib/bbn010. PMID 18344544. 
  6. ^ a b Griffiths-Jones, S; Bateman, A; Marshall, M; Khanna, A; Eddy, S. R. (2003). "Rfam: An RNA family database". Nucleic Acids Research. 31 (1): 439–41. doi:10.1093/nar/gkg006. PMC 165453Freely accessible. PMID 12520045. 
  7. ^ Griffiths-Jones, S; Grocock, R. J.; Van Dongen, S; Bateman, A; Enright, A. J. (2006). "MiRBase: MicroRNA sequences, targets and gene nomenclature". Nucleic Acids Research. 34 (Database issue): D140–4. doi:10.1093/nar/gkj112. PMC 1347474Freely accessible. PMID 16381832. 
  8. ^ a b Anon (2017). "ISCB Fellows". iscb.org. International Society for Computational Biology. Archived from the original on 2017-03-20. 
  9. ^ a b Alex Bateman publications indexed by Google Scholar Edit this at Wikidata
  10. ^ a b Chakradhar, Shraddha (2012). "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Archived from the original on 2013-03-30. 
  11. ^ Alex Bateman at DBLP Bibliography Server Edit this at Wikidata
  12. ^ Finn, R. D.; Mistry, J.; Schuster-Böckler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S. R.; Sonnhammer, E. L.; Bateman, A. (Jan 2006). "Pfam: clans, web tools and services" (Free full text). Nucleic Acids Research. 34 (Database issue): D247–D251. doi:10.1093/nar/gkj149. ISSN 0305-1048. PMC 1347511Freely accessible. PMID 16381856. 
  13. ^ Logan, D. W.; Sandal, M.; Gardner, P. P.; Manske, M.; Bateman, A. (2010). "Ten Simple Rules for Editing Wikipedia". PLOS Computational Biology. 6 (9): e1000941. doi:10.1371/journal.pcbi.1000941. PMC 2947980Freely accessible. PMID 20941386.  open access publication – free to read
  14. ^ "Bateman group < Research < EMBL-EBI". European Bioinformatics Institute. Archived from the original on 2013-10-01. 
  15. ^ Alex Bateman publications from Europe PubMed Central
  16. ^ Alex Bateman's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  17. ^ Burge, S.; Attwood, T. K.; Bateman, A.; Berardini, T. Z.; Cherry, M.; O'Donovan, C.; Xenarios, L.; Gaudet, P. (2012). "Biocurators and Biocuration: Surveying the 21st century challenges". Database. 2012: bar059. doi:10.1093/database/bar059. PMC 3308150Freely accessible. PMID 22434828. 
  18. ^ Bateman, A; Eddy, S. R.; Chothia, C (1996). "Members of the immunoglobulin superfamily in bacteria". Protein Science. 5 (9): 1939–41. doi:10.1002/pro.5560050923. PMC 2143528Freely accessible. PMID 8880921. 
  19. ^ Bateman, A; Jouet, M; MacFarlane, J; Du, J. S.; Kenwrick, S; Chothia, C (1996). "Outline structure of the human L1 cell adhesion molecule and the sites where mutations cause neurological disorders". The EMBO Journal. 15 (22): 6050–9. PMC 452426Freely accessible. PMID 8947027. 
  20. ^ Bateman, Alexander George (1997). Evolution of the structure and function of the immunoglobulin superfamily. ethos.bl.uk (PhD thesis). University of Cambridge. OCLC 879391333. 
  21. ^ Bateman, A; Murzin, A. G.; Teichmann, S. A. (1998). "Structure and distribution of pentapeptide repeats in bacteria". Protein Science. 7 (6): 1477–80. doi:10.1002/pro.5560070625. PMC 2144021Freely accessible. PMID 9655353. 
  22. ^ a b c "Archive page: Dr Alex Bateman - Wellcome Trust Sanger Institute". Wellcome Trust Sanger Institute. Archived from the original on 2014-10-13. 
  23. ^ Lander, Eric S.; et al. (15 February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011. 
  24. ^ "Alex Bateman < People & Groups < About us < EMBL-EBI". EBI. Archived from the original on 2013-10-01. 
  25. ^ Bateman, Alex (2012). "Why scientists should be publishing on Wikipedia". Wired UK. Archived from the original on 2012-07-09. 
  26. ^ Daub, J.; Gardner, P. P.; Tate, J.; Ramsköld, D.; Manske, M.; Scott, W. G.; Weinberg, Z.; Griffiths-Jones, S.; Bateman, A. (2008). "The RNA WikiProject: Community annotation of RNA families". RNA. 14 (12): 2462–2464. doi:10.1261/rna.1200508. PMC 2590952Freely accessible. PMID 18945806. 
  27. ^ Anon (2014). "15 years of "Bioinformatics"". Bioinformatics. 30 (6): 747. doi:10.1093/bioinformatics/btu076. PMID 24642573. 
  28. ^ "Officers and board of Directors ISCB". International Society for Computational Biology. Archived from the original on 2014-07-24. 
  29. ^ a b "Alex Bateman Wins 2010 Benjamin Franklin Award - Bio-IT World". www.bio-itworld.com. Archived from the original on 2012-08-14. 
  30. ^ "Alex wins the Benjamin Franklin award!". Xfam Blog. Archived from the original on 2010-04-28. 
  31. ^ "February 13, 2017: The International Society for Computational Biology Names Seven Members as the ISCB Fellows Class of 2017". www.iscb.org. Retrieved 13 February 2017.