Alex Bateman

Last updated

Alex Bateman
Alex Bateman ISMBECCB 2013.jpg
Bateman in 2013
Born
Alexander George Bateman

(1972-10-09) 9 October 1972 (age 51) [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]

Contents

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 at the MRC Laboratory of Molecular Biology (LMB) [18] [19] [20] on the evolution of the immunoglobulin protein superfamily. [21] [22] During this time, he also worked with Sean Eddy to discover novel protein domains using the HMMER software. [23]

Career and 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. [6] [23] He was also involved in providing protein analysis for the publication of the human genome. [23] [24]

As of 2012, he has been Head of Protein Sequence Resources at EMBL-EBI. [25]

Bateman has also been involved in promoting the use of Wikipedia within the science community [26] and in particular, community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through WikiProject RNA. [27]

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. [28] As of 2015, Bateman also serves on the ISCB Board of Directors. [29]

Awards and honours

Bateman was awarded the 2010 Benjamin Franklin Award in bioinformatics. [30] [31] He became the third former member of Richard Durbin's lab to win the award, following Sean Eddy and Ewan Birney. [30] [10] Bateman was elected an ISCB Fellow in 2017 by the International Society for Computational Biology. [8] [32]

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

Related Research Articles

<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, USA.

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.

<span class="mw-page-title-main">Pfam</span> Database of protein families

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 36.0, was released in September 2023 and contains 20,795 families.

<span class="mw-page-title-main">Ewan Birney</span> English businessman

John Frederick William Birney is joint director of EMBL's European Bioinformatics Institute (EMBL-EBI), in Hinxton, Cambridgeshire and deputy director general of the European Molecular Biology Laboratory (EMBL). He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH) and honorary professor of bioinformatics at the University of Cambridge. Birney has made significant contributions to genomics, through his development of innovative bioinformatics and computational biology tools. He previously served as an associate faculty member at the Wellcome Trust Sanger Institute.

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.

Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.

Anders Krogh is a bioinformatician at the University of Copenhagen, where he leads the university's bioinformatics center. He is known for his pioneering work on the use of hidden Markov models in bioinformatics, and is co-author of a widely used textbook in bioinformatics. In addition, he also co-authored one of the early textbooks on neural networks. His current research interests include promoter analysis, non-coding RNA, gene prediction and protein structure prediction.

<span class="mw-page-title-main">HMMER</span> Software package for sequence analysis

HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. It detects homology by comparing a profile-HMM to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the profile-HMM. Profile-HMMs are constructed from a multiple sequence alignment in the HMMER package using the hmmbuild program. The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. HMMER is a console utility ported to every major operating system, including different versions of Linux, Windows, and macOS.

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.

<span class="mw-page-title-main">Richard M. Durbin</span> British computational biologist

Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.

<span class="mw-page-title-main">Sean Eddy</span> American professor at Harvard University

Sean Roberts Eddy is Professor of Molecular & Cellular Biology and of Applied Mathematics at Harvard University. Previously he was based at the Janelia Research Campus from 2006 to 2015 in Virginia. His research interests are in bioinformatics, computational biology and biological sequence analysis. As of 2016 projects include the use of Hidden Markov models in HMMER, Infernal Pfam and Rfam.

<span class="mw-page-title-main">Cyrus Chothia</span> English biochemist (1942–2019)

Cyrus Homi Chothia was an English biochemist who was an emeritus scientist at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) at the University of Cambridge and emeritus fellow of Wolfson College, Cambridge.

<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.

<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.

<span class="mw-page-title-main">Burkhard Rost</span> German computational biology researcher

Burkhard Rost is a scientist leading the Department for Computational Biology & Bioinformatics at the Faculty of Informatics of the Technical University of Munich (TUM). Rost chairs the Study Section Bioinformatics Munich involving the TUM and the Ludwig Maximilian University of Munich (LMU) in Munich. From 2007-2014 Rost was President of the International Society for Computational Biology (ISCB).

<span class="mw-page-title-main">Gary Stormo</span> American geneticist (born 1950)

Gary Stormo is an American geneticist and currently Joseph Erlanger Professor in the Department of Genetics and the Center for Genome Sciences and Systems Biology at Washington University School of Medicine in St Louis. He is considered one of the pioneers of bioinformatics and genomics. His research combines experimental and computational approaches in order to identify and predict regulatory sequences in DNA and RNA, and their contributions to the regulatory networks that control gene expression.

<span class="mw-page-title-main">Tim Hubbard</span> Professor of Bioinformatics at Kings College London

Timothy John Phillip Hubbard is a Professor of Bioinformatics at King's College London, Head of Genome Analysis at Genomics England and Honorary Faculty at the Wellcome Trust Sanger Institute in Cambridge, UK. From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.

<span class="mw-page-title-main">Sarah Teichmann</span> German bioinformatician

Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.

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.

Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.

References

  1. ↑ Alex Bateman at Library of Congress
  2. 1 2 "Alex Bateman: Senior Team Leader Protein Sequence Resources and Group Leader Bateman Research Group". Uniprot.org. Archived from the original on 16 March 2015.
  3. 1 2 "Alex Bateman Publons". Publons.com. Archived from the original on 16 March 2015.
  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   308855 . PMID   14681378. Open Access logo PLoS transparent.svg
  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. 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.
  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   1347474 . PMID   16381832.
  8. 1 2 Anon (2017). "ISCB Fellows". iscb.org. International Society for Computational Biology. Archived from the original on 20 March 2017.
  9. 1 2 Alex Bateman publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  10. 1 2 Chakradhar, Shraddha (2012). "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Archived from the original on 30 March 2013.
  11. ↑ Alex Bateman at DBLP Bibliography Server OOjs UI icon edit-ltr-progressive.svg
  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. (January 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.
  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. Bibcode:2010PLSCB...6E0941L. doi: 10.1371/journal.pcbi.1000941 . PMC   2947980 . PMID   20941386. Open Access logo PLoS transparent.svg
  14. ↑ "Bateman group < Research < EMBL-EBI". European Bioinformatics Institute. Archived from the original on 1 October 2013.
  15. ↑ Alex Bateman publications from Europe PubMed Central
  16. ↑ Alex Bateman's publications indexed by the Scopus bibliographic database. (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   3308150 . PMID   22434828.
  18. ↑ "Family values – People – EMBO". 8 June 2021. Retrieved 14 July 2023.
  19. ↑ 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.
  20. ↑ 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. doi:10.1002/j.1460-2075.1996.tb00993.x. PMC   452426 . PMID   8947027.
  21. ↑ Bateman, Alexander George (1997). Evolution of the structure and function of the immunoglobulin superfamily. ethos.bl.uk (PhD thesis). University of Cambridge. OCLC   879391333.
  22. ↑ 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.
  23. 1 2 3 "Archive page: Dr Alex Bateman - Wellcome Trust Sanger Institute". Wellcome Trust Sanger Institute. Archived from the original on 13 October 2014.
  24. ↑ 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 . hdl: 2027.42/62798 . PMID   11237011.
  25. ↑ "Alex Bateman < People & Groups < About us < EMBL-EBI". EBI. Archived from the original on 1 October 2013.
  26. ↑ Bateman, Alex (2012). "Why scientists should be publishing on Wikipedia". Wired UK . Archived from the original on 9 July 2012.
  27. ↑ 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.
  28. ↑ Anon (2014). "15 years of "Bioinformatics"". Bioinformatics. 30 (6): 747. doi: 10.1093/bioinformatics/btu076 . PMID   24642573.
  29. ↑ "Officers and board of Directors ISCB". International Society for Computational Biology. Archived from the original on 24 July 2014.
  30. 1 2 "Alex Bateman Wins 2010 Benjamin Franklin Award - Bio-IT World". www.bio-itworld.com. Archived from the original on 14 August 2012.
  31. ↑ "Alex wins the Benjamin Franklin award!". Xfam Blog. April 2010. Archived from the original on 28 April 2010.
  32. ↑ "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.
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