Alex Bateman

Alex Bateman

Alex Bateman speaking at the Intelligent Systems for Molecular Biology (ISMB) conference in 2013.
Born Alexander George Bateman
Institutions
Alma mater
Thesis Evolution of the structure and function of the immunoglobulin superfamily (1997)
Doctoral advisor Cyrus Chothia
Doctoral students
  • Benjamin Schuster-Bockler[1]
  • Marija Buljan[2][3]
  • Lars Barquist[4]
Known for
Notable awards Benjamin Franklin Award (2010)
Website
www.ebi.ac.uk/about/people/alex-bateman

Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at EMBL-EBI.[11][12] He has led the development of the Pfam biological database[13] 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.[14][15][16][17][18][19]

Education

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[20][21] on the evolution of the immunoglobulin protein superfamily.[22][23] During this time, he also worked with Sean Eddy to discover novel protein domains using the HMMER software.[24]

Research

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.[9][24] He was also involved in providing protein analysis for the publication of the human genome.[24][25]

As of 2012, he has been Head of Protein Sequence Resources at EMBL-EBI.[26]

Bateman has also been involved in promoting the use of Wikipedia within the science community[27] and in particular, community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through WikiProject RNA.[28]

Awards and honours

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][31]

Bateman was 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.[5][6] In 2014, he was appointed one of the first Honorary Editors of Bioinformatics.[32] As of 2015, Bateman also serves on the International Society for Computational Biology (ISCB) Board of Directors.[33]

References

  1. ↑ Schuster-Bockler, Benjamin (2008). The role of protein interactions in evolution and disease (PhD thesis). University of Cambridge.
  2. ↑ Buljan, Marija (2011). Mechanisms of change in protein architecture (PhD thesis). University of Cambridge.
  3. ↑ Buljan, M; Frankish, A; Bateman, A (2010). "Quantifying the mechanisms of domain gain in animal proteins". Genome Biology 11 (7): R74. doi:10.1186/gb-2010-11-7-r74. PMC 2926785. PMID 20633280.
  4. ↑ Barquist, Lars (2014). High-throughput experimental and computational studies of bacterial evolution (PhD thesis). University of Cambridge.
  5. 1 2 "Alex Bateman: Senior Team Leader Protein Sequence Resources and Group Leader Bateman Research Group". Uniprot.org. Archived from the original on 2015-03-16.
  6. 1 2 "Alex Bateman Publons". Publons.com. Archived from the original on 2015-03-16.
  7. ↑ 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 308855. PMID 14681378.
  8. ↑ 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.
  9. 1 2 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 165453. PMID 12520045.
  10. ↑ 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 1347474. PMID 16381832.
  11. ↑ Alex Bateman's publications indexed by Google Scholar, a service provided by Google
  12. ↑ Alex Bateman's publications indexed by the DBLP Bibliography Server at the University of Trier
  13. ↑ 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 1347511. PMID 16381856.
  14. ↑ 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 2947980. PMID 20941386.
  15. ↑ "Bateman group < Research < EMBL-EBI". European Bioinformatics Institute. Archived from the original on 2013-10-01.
  16. ↑ Alex Bateman publications from Europe PubMed Central
  17. ↑ Alex Bateman's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  18. ↑ 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 3308150. PMID 22434828.
  19. ↑ Alex Bateman on Twitter
  20. ↑ 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 2143528. PMID 8880921.
  21. ↑ 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 452426. PMID 8947027.
  22. ↑ Bateman, Alexander George (1997). Evolution of the structure and function of the immunoglobulin superfamily (PhD thesis). University of Cambridge.
  23. ↑ 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 2144021. PMID 9655353.
  24. 1 2 3 "Archive page: Dr Alex Bateman - Wellcome Trust Sanger Institute". Wellcome Trust Sanger Institute. Archived from the original on 2014-10-13.
  25. ↑ 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.
  26. ↑ "Alex Bateman < People & Groups < About us < EMBL-EBI". EBI. Archived from the original on 2013-10-01.
  27. ↑ "Alex Bateman: Why scientists should be publishing on Wikipedia". Wired UK. Archived from the original on 2012-07-09.
  28. ↑ 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 2590952. PMID 18945806.
  29. 1 2 "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. ↑ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Archived from the original on 2013-03-30.
  32. ↑ Anon (2014). "15 years of "Bioinformatics"". Bioinformatics 30 (6): 747. doi:10.1093/bioinformatics/btu076. PMID 24642573.
  33. ↑ "Officers and board of Directors ISCB". International Society for Computational Biology. Archived from the original on 2014-07-24.
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