Alex Bateman

{{Short description|British bioinformatician}}

{{Use dmy dates|date=April 2022}}

{{Infobox scientist

| name = Alex Bateman

| birth_name = Alexander George Bateman

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| image = Alex Bateman ISMBECCB 2013.jpg

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| caption = Bateman in 2013

| birth_date = {{Birth date and age|1972|10|09|df=y}}{{LCAuth|n2013022816|Alex Bateman||}}

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| thesis_title = Evolution of the structure and function of the immunoglobulin superfamily

| thesis_url = http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596466

| thesis_year = 1997

| doctoral_advisor = Cyrus Chothia

| academic_advisors = Richard M. Durbin

| doctoral_students =

| notable_students =

| known_for = {{Plainlist|

  • UniProt{{cite web|title=Alex Bateman: Senior Team Leader Protein Sequence Resources and Group Leader Bateman Research Group|publisher=Uniprot.org|url=https://www.uniprot.org/help/bateman|archive-date=2015-03-16|archive-url=https://web.archive.org/web/20150316083837/http://www.uniprot.org/help/bateman}}
  • Pfam{{Cite journal | first1 = A. | last1 = Bateman | author-link1 = Alex Bateman| first2 = L. | last2 = Coin | first3 = R. | last3 = Durbin | author-link3 = Richard M. Durbin | first4 = R. D. | last4 = Finn | first5 = V. | last5 = Hollich | first6 = S. | last6 = Griffiths-Jones | first7 = A. | last7 = Khanna | first8 = M. | last8 = Marshall | first9 = S. | last10 = Sonnhammer | last9 = Moxon | first10 = E. L. | last11 = Studholme | first11 = D. J. | last12 = Yeats | first12 = C. | last13 = Eddy | first13 = S. R.| author-link13 = Sean Eddy| title = The Pfam protein families database| journal = Nucleic Acids Research| volume = 32| issue = Database issue| pages = 138D–1141| year=2004 | issn = 0305-1048| pmid = 14681378| doi = 10.1093/nar/gkh121| pmc = 308855}} {{open access}}{{Cite journal | pmid = 18344544| year = 2008| last1 = Sammut| first1 = S. J.| title = Pfam 10 years on: 10,000 families and still growing| journal = Briefings in Bioinformatics| volume = 9| issue = 3| pages = 210–9| last2 = Finn| first2 = R. D.| last3 = Bateman| first3 = A| doi = 10.1093/bib/bbn010| doi-access = free}}
  • Rfam
  • MiRBase{{Cite journal | pmid = 16381832| pmc = 1347474| year = 2006| last1 = Griffiths-Jones| first1 = S| title = MiRBase: MicroRNA sequences, targets and gene nomenclature| journal = Nucleic Acids Research| volume = 34| issue = Database issue| pages = D140-4| last2 = Grocock| first2 = R. J.| last3 = Van Dongen| first3 = S| last4 = Bateman| first4 = A| last5 = Enright| first5 = A. J.| doi = 10.1093/nar/gkj112}}}}

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| website = {{URL|http://www.ebi.ac.uk/about/people/alex-bateman}}

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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.{{Google Scholar id}}{{DBLP|name=Alex Bateman}} He has led the development of the Pfam biological database{{Cite journal

| last1 = Finn | first1 = R. D.

| last2 = Mistry | first2 = J.

| last3 = Schuster-Böckler | first3 = B.

| last4 = Griffiths-Jones | first4 = S.

| last5 = Hollich | first5 = V.

| last6 = Lassmann | first6 = T.

| last7 = Moxon | first7 = S.

| last8 = Marshall | first8 = M.

| last9 = Khanna | first9 = A.

| last10 = Durbin | first10 = R.

| last11 = Eddy | first11 = S. R.

| last12 = Sonnhammer | first12 = E. L.

| last13 = Bateman | first13 = A.

| title = Pfam: clans, web tools and services

| format = Free full text

| journal = Nucleic Acids Research

| volume = 34

| issue = Database issue

| pages = D247–D251

| date=Jan 2006 | issn = 0305-1048

| pmid = 16381856

| doi = 10.1093/nar/gkj149

| pmc = 1347511

}} 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.{{Cite journal

| last1 = Logan | first1 = D. W.

| last2 = Sandal | first2 = M.

| last3 = Gardner | first3 = P. P.

| last4 = Manske | first4 = M.

| author-link4 = Magnus Manske

| last5 = Bateman | first5 = A.

| author-link5 = Alex Bateman

| title = Ten Simple Rules for Editing Wikipedia

| doi = 10.1371/journal.pcbi.1000941

| journal = PLOS Computational Biology

| volume = 6

| issue = 9

| pages = e1000941

| year = 2010

| pmid = 20941386

| pmc =2947980

| bibcode = 2010PLSCB...6E0941L

| doi-access = free

}} {{open access}}{{cite web|title=Bateman group < Research < EMBL-EBI|url=http://www.ebi.ac.uk/research/bateman|archive-date=2013-10-01|publisher=European Bioinformatics Institute|archive-url=https://web.archive.org/web/20131001121800/http://www.ebi.ac.uk/research/bateman}}{{EuropePMC|ORCID=0000-0002-6982-4660}}{{Scopus|id=7102456158}}{{Cite journal | last1 = Burge | first1 = S. | last2 = Attwood | first2 = T. K. | author-link2 = Terri Attwood| last3 = Bateman | first3 = A. | author-link3 = Alex Bateman| last4 = Berardini | first4 = T. Z. | last5 = Cherry | first5 = M. | last6 = O'Donovan | first6 = C. | last7 = Xenarios | first7 = L. | last8 = Gaudet | first8 = P. | doi = 10.1093/database/bar059 | title = Biocurators and Biocuration: Surveying the 21st century challenges | journal = Database | volume = 2012 | pages = bar059 | year = 2012 | pmid = 22434828| pmc =3308150 }}

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){{Cite web |date=2021-06-08 |title=Family values – People – EMBO |url=https://www.embo.org/people/family-values/ |access-date=2023-07-14 |language=en-GB}}{{Cite journal | pmid = 8880921| pmc = 2143528| year = 1996| last1 = Bateman | first1 = A | author-link1 = Alex Bateman| title = Members of the immunoglobulin superfamily in bacteria| journal = Protein Science| volume = 5| issue = 9| pages = 1939–41| last2 = Eddy| first2 = S. R.|author-link2 = Sean Eddy| last3 = Chothia| first3 = C|author-link3= Cyrus Chothia| doi = 10.1002/pro.5560050923}}{{Cite journal | pmid = 8947027| pmc = 452426| year = 1996| last1 = Bateman| first1 = A| title = Outline structure of the human L1 cell adhesion molecule and the sites where mutations cause neurological disorders| journal = The EMBO Journal| volume = 15| issue = 22| pages = 6050–9| last2 = Jouet| first2 = M| last3 = MacFarlane| first3 = J| last4 = Du| first4 = J. S.| last5 = Kenwrick| first5 = S| last6 = Chothia| first6 = C| doi = 10.1002/j.1460-2075.1996.tb00993.x}} on the evolution of the immunoglobulin protein superfamily.{{cite thesis |degree=PhD |first=Alexander George|last=Bateman |title=Evolution of the structure and function of the immunoglobulin superfamily |publisher=University of Cambridge |date=1997|oclc=879391333 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596466|website=ethos.bl.uk}}{{Cite journal | pmid = 9655353| pmc = 2144021| year = 1998| last1 = Bateman| first1 = A| author-link1 = Alex Bateman| title = Structure and distribution of pentapeptide repeats in bacteria| journal = Protein Science| volume = 7| issue = 6| pages = 1477–80| last2 = Murzin| first2 = A. G.| last3 = Teichmann| first3 = S. A.| author-link3 = Sarah Teichmann| doi = 10.1002/pro.5560070625}} During this time, he also worked with Sean Eddy to discover novel protein domains using the HMMER software.{{cite web|title=Archive page: Dr Alex Bateman - Wellcome Trust Sanger Institute|url=https://www.sanger.ac.uk/research/faculty/abateman/|publisher=Wellcome Trust Sanger Institute|archive-date= 2014-10-13|archive-url=https://web.archive.org/web/20141013222743/http://www.sanger.ac.uk/research/faculty/abateman/}}

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.{{Cite journal

| pmid = 12520045

| pmc = 165453

| year = 2003

| last1 = Griffiths-Jones

| first1 = S

| title = Rfam: An RNA family database

| journal = Nucleic Acids Research

| volume = 31

| issue = 1

| pages = 439–41

| last2 = Bateman

| first2 = A

| last3 = Marshall

| first3 = M

| last4 = Khanna

| first4 = A

| last5 = Eddy

| first5 = S. R.

| doi=10.1093/nar/gkg006

}} He was also involved in providing protein analysis for the publication of the human genome.{{cite journal|display-authors=1|last1=Lander|first1=Eric S.|last2=Linton|first2=Lauren M.|last3=Birren|first3=Bruce|last4=Nusbaum|first4=Chad|last5=Zody|first5=Michael C.|last6=Baldwin|first6=Jennifer|last7=Devon|first7=Keri|last8=Dewar|first8=Ken|last9=Doyle|first9=Michael|last10=FitzHugh|first10=William|last11=Funke|first11=Roel|last12=Gage|first12=Diane|last13=Harris|first13=Katrina|last14=Heaford|first14=Andrew|last15=Howland|first15=John|last16=Kann|first16=Lisa|last17=Lehoczky|first17=Jessica|last18=LeVine|first18=Rosie|last19=McEwan|first19=Paul|last20=McKernan|first20=Kevin|last21=Meldrim|first21=James|last22=Mesirov|first22=Jill P.|last23=Miranda|first23=Cher|last24=Morris|first24=William|last25=Naylor|first25=Jerome|last26=Raymond|first26=Christina|last27=Rosetti|first27=Mark|last28=Santos|first28=Ralph|last29=Sheridan|first29=Andrew|last30=Sougnez|first30=Carrie|last31=Stange-Thomann|first31=Nicole|last32=Stojanovic|first32=Nikola|last33=Subramanian|first33=Aravind|last34=Wyman|first34=Dudley|last35=Rogers|first35=Jane|last36=Sulston|first36=John|last37=Ainscough|first37=Rachael|last38=Beck|first38=Stephan|last39=Bentley|first39=David|last40=Burton|first40=John|last41=Clee|first41=Christopher|last42=Carter|first42=Nigel|last43=Coulson|first43=Alan|last44=Deadman|first44=Rebecca|last45=Deloukas|first45=Panos|last46=Dunham|first46=Andrew|last47=Dunham|first47=Ian|last48=Durbin|first48=Richard|last49=French|first49=Lisa|last50=Grafham|first50=Darren|last51=Gregory|first51=Simon|last52=Hubbard|first52=Tim|last53=Humphray|first53=Sean|last54=Hunt|first54=Adrienne|last55=Jones|first55=Matthew|last56=Lloyd|first56=Christine|last57=McMurray|first57=Amanda|last58=Matthews|first58=Lucy|last59=Mercer|first59=Simon|last60=Milne|first60=Sarah|last61=Mullikin|first61=James C.|last62=Mungall|first62=Andrew|last63=Plumb|first63=Robert|last64=Ross|first64=Mark|last65=Shownkeen|first65=Ratna|last66=Sims|first66=Sarah|last67=Waterston|first67=Robert H.|last68=Wilson|first68=Richard K.|last69=Hillier|first69=LaDeana W.|last70=McPherson|first70=John D.|last71=Marra|first71=Marco A.|last72=Mardis|first72=Elaine R.|last73=Fulton|first73=Lucinda A.|last74=Chinwalla|first74=Asif T.|last75=Pepin|first75=Kymberlie H.|last76=Gish|first76=Warren R.|last77=Chissoe|first77=Stephanie L.|last78=Wendl|first78=Michael C.|last79=Delehaunty|first79=Kim D.|last80=Miner|first80=Tracie L.|last81=Delehaunty|first81=Andrew|last82=Kramer|first82=Jason B.|last83=Cook|first83=Lisa L.|last84=Fulton|first84=Robert S.|last85=Johnson|first85=Douglas L.|last86=Minx|first86=Patrick J.|last87=Clifton|first87=Sandra W.|last88=Hawkins|first88=Trevor|last89=Branscomb|first89=Elbert|last90=Predki|first90=Paul|last91=Richardson|first91=Paul|last92=Wenning|first92=Sarah|last93=Slezak|first93=Tom|last94=Doggett|first94=Norman|last95=Cheng|first95=Jan-Fang|last96=Olsen|first96=Anne|last97=Lucas|first97=Susan|last98=Elkin|first98=Christopher|last99=Uberbacher|first99=Edward|last100=Frazier|first100=Marvin|last101=Gibbs|first101=Richard A.|last102=Muzny|first102=Donna M.|last103=Scherer|first103=Steven E.|last104=Bouck|first104=John B.|last105=Sodergren|first105=Erica J.|last106=Worley|first106=Kim C.|last107=Rives|first107=Catherine M.|last108=Gorrell|first108=James H.|last109=Metzker|first109=Michael L.|last110=Naylor|first110=Susan L.|last111=Kucherlapati|first111=Raju S.|last112=Nelson|first112=David L.|last113=Weinstock|first113=George M.|last114=Sakaki|first114=Yoshiyuki|last115=Fujiyama|first115=Asao|last116=Hattori|first116=Masahira|last117=Yada|first117=Tetsushi|last118=Toyoda|first118=Atsushi|last119=Itoh|first119=Takehiko|last120=Kawagoe|first120=Chiharu|last121=Watanabe|first121=Hidemi|last122=Totoki|first122=Yasushi|last123=Taylor|first123=Todd|last124=Weissenbach|first124=Jean|last125=Heilig|first125=Roland|last126=Saurin|first126=William|last127=Artiguenave|first127=Francois|last128=Brottier|first128=Philippe|last129=Bruls|first129=Thomas|last130=Pelletier|first130=Eric|last131=Robert|first131=Catherine|last132=Wincker|first132=Patrick|last133=Rosenthal|first133=André|last134=Platzer|first134=Matthias|last135=Nyakatura|first135=Gerald|last136=Taudien|first136=Stefan|last137=Rump|first137=Andreas|last138=Smith|first138=Douglas R.|last139=Doucette-Stamm|first139=Lynn|last140=Rubenfield|first140=Marc|last141=Weinstock|first141=Keith|last142=Lee|first142=Hong Mei|last143=Dubois|first143=JoAnn|last144=Yang|first144=Huanming|last145=Yu|first145=Jun|last146=Wang|first146=Jian|last147=Huang|first147=Guyang|last148=Gu|first148=Jun|last149=Hood|first149=Leroy|last150=Rowen|first150=Lee|last151=Madan|first151=Anup|last152=Qin|first152=Shizen|last153=Davis|first153=Ronald W.|last154=Federspiel|first154=Nancy A.|last155=Abola|first155=A. Pia|last156=Proctor|first156=Michael J.|last157=Roe|first157=Bruce A.|last158=Chen|first158=Feng|last159=Pan|first159=Huaqin|last160=Ramser|first160=Juliane|last161=Lehrach|first161=Hans|last162=Reinhardt|first162=Richard|last163=McCombie|first163=W. Richard|last164=de la Bastide|first164=Melissa|last165=Dedhia|first165=Neilay|last166=Blöcker|first166=Helmut|last167=Hornischer|first167=Klaus|last168=Nordsiek|first168=Gabriele|last169=Agarwala|first169=Richa|last170=Aravind|first170=L.|last171=Bailey|first171=Jeffrey A.|last172=Bateman|first172=Alex|last173=Batzoglou|first173=Serafim|last174=Birney|first174=Ewan|last175=Bork|first175=Peer|last176=Brown|first176=Daniel G.|last177=Burge|first177=Christopher B.|last178=Cerutti|first178=Lorenzo|last179=Chen|first179=Hsiu-Chuan|last180=Church|first180=Deanna|last181=Clamp|first181=Michele|last182=Copley|first182=Richard R.|last183=Doerks|first183=Tobias|last184=Eddy|first184=Sean R.|last185=Eichler|first185=Evan E.|last186=Furey|first186=Terrence S.|last187=Galagan|first187=James|last188=Gilbert|first188=James G. R.|last189=Harmon|first189=Cyrus|last190=Hayashizaki|first190=Yoshihide|last191=Haussler|first191=David|last192=Hermjakob|first192=Henning|last193=Hokamp|first193=Karsten|last194=Jang|first194=Wonhee|last195=Johnson|first195=L. Steven|last196=Jones|first196=Thomas A.|last197=Kasif|first197=Simon|last198=Kaspryzk|first198=Arek|last199=Kennedy|first199=Scot|last200=Kent|first200=W. James|last201=Kitts|first201=Paul|last202=Koonin|first202=Eugene V.|last203=Korf|first203=Ian|last204=Kulp|first204=David|last205=Lancet|first205=Doron|last206=Lowe|first206=Todd M.|last207=McLysaght|first207=Aoife|last208=Mikkelsen|first208=Tarjei|last209=Moran|first209=John V.|last210=Mulder|first210=Nicola|last211=Pollara|first211=Victor J.|last212=Ponting|first212=Chris P.|last213=Schuler|first213=Greg|last214=Schultz|first214=Jörg|last215=Slater|first215=Guy|last216=Smit|first216=Arian F. A.|last217=Stupka|first217=Elia|last218=Szustakowki|first218=Joseph|last219=Thierry-Mieg|first219=Danielle|last220=Thierry-Mieg|first220=Jean|last221=Wagner|first221=Lukas|last222=Wallis|first222=John|last223=Wheeler|first223=Raymond|last224=Williams|first224=Alan|last225=Wolf|first225=Yuri I.|last226=Wolfe|first226=Kenneth H.|last227=Yang|first227=Shiaw-Pyng|last228=Yeh|first228=Ru-Fang|last229=Collins|first229=Francis|last230=Guyer|first230=Mark S.|last231=Peterson|first231=Jane|last232=Felsenfeld|first232=Adam|last233=Wetterstrand|first233=Kris A.|last234=Myers|first234=Richard M.|last235=Schmutz|first235=Jeremy|last236=Dickson|first236=Mark|last237=Grimwood|first237=Jane|last238=Cox|first238=David R.|last239=Olson|first239=Maynard V.|last240=Kaul|first240=Rajinder|last241=Raymond|first241=Christopher|last242=Shimizu|first242=Nobuyoshi|last243=Kawasaki|first243=Kazuhiko|last244=Minoshima|first244=Shinsei|last245=Evans|first245=Glen A.|last246=Athanasiou|first246=Maria|last247=Schultz|first247=Roger|last248=Patrinos|first248=Aristides|last249=Morgan|first249=Michael J.|title=Initial sequencing and analysis of the human genome|journal=Nature|date=15 February 2001|volume=409|issue=6822|pages=860–921|doi=10.1038/35057062|pmid=11237011|doi-access=free|hdl=2027.42/62798|hdl-access=free}}

As of 2012, he has been Head of Protein Sequence Resources at EMBL-EBI.{{cite web|title=Alex Bateman < People & Groups < About us < EMBL-EBI|url=http://www.ebi.ac.uk/about/people/alex-bateman|archive-date=2013-10-01|archive-url=https://web.archive.org/web/20131001200201/http://www.ebi.ac.uk/about/people/alex-bateman|publisher=EBI}}

Bateman has also been involved in promoting the use of Wikipedia within the science community{{cite magazine|first=Alex|last=Bateman|year=2012|title=Why scientists should be publishing on Wikipedia|magazine=Wired UK|url=https://www.wired.co.uk/magazine/archive/2012/05/ideas-bank/scientists-should-be-publishing-on-wikipedia|archive-url=https://web.archive.org/web/20120709062931/http://www.wired.co.uk/magazine/archive/2012/05/ideas-bank/scientists-should-be-publishing-on-wikipedia|archive-date=2012-07-09}} and in particular, community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through WikiProject RNA.{{Cite journal

| last1 = Daub | first1 = J.

| last2 = Gardner | first2 = P. P.

| last3 = Tate | first3 = J.

| last4 = Ramsköld | first4 = D.

| last5 = Manske | first5 = M.

| author-link5 = Magnus Manske

| last6 = Scott | first6 = W. G.

| last7 = Weinberg | first7 = Z.

| last8 = Griffiths-Jones | first8 = S.

| last9 = Bateman | first9 = A.

| doi = 10.1261/rna.1200508

| title = The RNA WikiProject: Community annotation of RNA families

| journal = RNA

| volume = 14

| issue = 12

| pages = 2462–2464

| year = 2008

| pmid = 18945806

| pmc =2590952

}}

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.{{cite web|url=https://publons.com/author/259342/alex-bateman|title=Alex Bateman Publons|publisher=Publons.com|archive-url=https://web.archive.org/web/20150316092353/https://publons.com/author/259342/alex-bateman|archive-date=2015-03-16}} In 2014, he was appointed one of the first Honorary Editors of Bioinformatics.{{Cite journal

| author = Anon

| pmid = 24642573

| year = 2014

| title = 15 years of "Bioinformatics"

| journal = Bioinformatics

| volume = 30

| issue = 6

| pages = 747

| doi = 10.1093/bioinformatics/btu076

| doi-access = free

}} As of 2015, Bateman also serves on the ISCB Board of Directors.{{cite web|title=Officers and board of Directors ISCB|url=http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors|archive-date=2014-07-24|archive-url=https://web.archive.org/web/20140724002222/http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors|publisher=International Society for Computational Biology}}

Awards and honours

Bateman was awarded the 2010 Benjamin Franklin Award in bioinformatics.{{cite web|title=Alex Bateman Wins 2010 Benjamin Franklin Award - Bio-IT World|url=http://www.bio-itworld.com/2010/04/01/franklin-award.html|publisher=www.bio-itworld.com|archive-url=https://web.archive.org/web/20120814000046/http://www.bio-itworld.com/2010/04/01/franklin-award.html|archive-date=2012-08-14}}{{cite web|title=Alex wins the Benjamin Franklin award!|publisher=Xfam Blog|url=https://xfam.wordpress.com/2010/04/01/alex-wins-the-benjamin-franklin-award/|archive-url=https://web.archive.org/web/20100428005754/http://xfam.wordpress.com/2010/04/01/alex-wins-the-benjamin-franklin-award/|archive-date=2010-04-28|date=April 2010}} He became the third former member of Richard Durbin's lab to win the award, following Sean Eddy and Ewan Birney.{{cite web|first=Shraddha|last=Chakradhar|year=2012|title=Heng Li Credits Durbin Pedigree in Accepting Franklin Award|url=http://www.bio-itworld.com/news/04/26/12/Heng-Li-credits-Durbin-pedigree-Franklin-Award.html|archive-date=2013-03-30|archive-url=https://web.archive.org/web/20130330132717/http://www.bio-itworld.com/news/04/26/12/Heng-Li-credits-Durbin-pedigree-Franklin-Award.html|publisher=bio-itworld.com}}

Bateman was elected an ISCB Fellow in 2017 by the International Society for Computational Biology.{{cite web|archive-url=https://web.archive.org/web/20170320114530/https://www.iscb.org/iscb-fellows |archive-date=2017-03-20 |url=https://www.iscb.org/iscb-fellows |website=iscb.org |title=ISCB Fellows |publisher=International Society for Computational Biology |author=Anon |year=2017 |url-status=dead }}{{cite web|title=February 13, 2017: The International Society for Computational Biology Names Seven Members as the ISCB Fellows Class of 2017|url=https://www.iscb.org/iscb-news-items/3067-2017-feb13-iscb-fellows-class-2017|website=www.iscb.org|access-date=13 February 2017}}

File:Alex_Bateman_Cyrus_Chothia_ISMB_2015.jpg

References