Tim Hubbard
{{Short description|Professor of Bioinformatics at King's College London}}
{{Infobox scientist
| name = Tim Hubbard
| birth_name = Timothy John Phillip Hubbard
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| image = Tim Hubbard (8243443127).jpg
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| fields = {{Plainlist|
| workplaces = {{Plainlist|
- King's College London
- Genomics England{{cite web|archive-url=https://web.archive.org/web/20150112230343/http://www.genomicsengland.co.uk/genomics-england-publishes-results-of-its-annotation-assessment/|archive-date=2015-01-12|title=Genomics England publishes results of its annotation assessment|work=Genomics England |url=http://www.genomicsengland.co.uk/genomics-england-publishes-results-of-its-annotation-assessment/|year=2014}}
- NHS England
- Wellcome Trust Sanger Institute
}}
| patrons =
| alma_mater = {{Plainlist|
- University of Cambridge (BA)
- Birkbeck College, London (PhD)}}
| thesis_title = The design, expression and characterisation of a novel protein
| thesis_url = http://catalogue.ulrls.lon.ac.uk/record=b1582475
| thesis_year = 1988
| doctoral_advisor = Tom Blundell
| academic_advisors =
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| notable_students =
| known_for = {{Plainlist|
- SCOP database{{Cite journal | last1 = Murzin | first1 = A. G. | last2 = Brenner | first2 = S. | author-link2 = Steven E. Brenner | last3 = Hubbard | first3 = T. | author-link3 = Tim Hubbard | last4 = Chothia | first4 = C. | author-link4 = Cyrus Chothia | title = SCOP: A structural classification of proteins database for the investigation of sequences and structures | journal = Journal of Molecular Biology | volume = 247 | issue = 4 | pages = 536–540 | year = 1995 | doi = 10.1016/S0022-2836(05)80134-2 | pmid = 7723011 | url = http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf | url-status = dead | archive-url = https://web.archive.org/web/20120426170732/http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf | archive-date = 2012-04-26 }}
- GENCODE{{Cite journal
| pmid = 16925838
| year = 2006
| last1 = Harrow
| first1 = J
| title = GENCODE: Producing a reference annotation for ENCODE
| journal = Genome Biology
| volume = 7
| pages = S4.1–9
| last2 = Denoeud
| first2 = F
| last3 = Frankish
| first3 = A
| last4 = Reymond
| first4 = A
| last5 = Chen
| first5 = C. K.
| last6 = Chrast
| first6 = J
| last7 = Lagarde
| first7 = J
| last8 = Gilbert
| first8 = J. G.
| last9 = Storey
| first9 = R
| last10 = Swarbreck
| first10 = D
| last11 = Rossier
| first11 = C
| last12 = Ucla
| first12 = C
| last13 = Hubbard
| first13 = T
| last14 = Antonarakis
| first14 = S. E.
| last15 = Guigo
| first15 = R
| issue = Suppl 1
| doi = 10.1186/gb-2006-7-s1-s4
| pmc = 1810553
| doi-access = free
}}
| last1 = Hubbard | first1 = T.
| author-link1 = Tim Hubbard
| last2 = Barker | first2 = D.
| last3 = Birney | first3 = E.
| author-link3 = Ewan Birney
| last4 = Cameron | first4 = G.
| last5 = Chen | first5 = Y.
| last6 = Clark | first6 = L.
| last7 = Cox | first7 = T.
| last8 = Cuff | first8 = J.
| last9 = Curwen | first9 = V.
| last10 = Down | first10 = T.
| last11 = Durbin | first11 = R.
| last12 = Eyras | first12 = E.
| last13 = Gilbert | first13 = J.
| last14 = Hammond | first14 = M.
| last15 = Huminiecki | first15 = L.
| last16 = Kasprzyk | first16 = A.
| last17 = Lehvaslaiho | first17 = H.
| last18 = Lijnzaad | first18 = P.
| last19 = Melsopp | first19 = C.
| last20 = Mongin | first20 = E.
| last21 = Pettett | first21 = R.
| last22 = Pocock | first22 = M.
| last23 = Potter | first23 = S.
| last24 = Rust | first24 = A.
| last25 = Schmidt | first25 = E.
| last26 = Searle | first26 = S.
| last27 = Slater | first27 = G.
| last28 = Smith | first28 = J.
| last29 = Spooner | first29 = W.
| last30 = Stabenau | first30 = A.
| title = The Ensembl genome database project
| journal = Nucleic Acids Research
| volume = 30
| issue = 1
| pages = 38–41
| year = 2002
| pmid = 11752248
| pmc = 99161 | doi=10.1093/nar/30.1.38
| pmid = 10526346
| year = 1999
| last1 = Moult
| first1 = J
| title = Critical assessment of methods of protein structure prediction (CASP): Round III
| journal = Proteins
| volume = Suppl 3
| pages = 2–6
| last2 = Hubbard
| first2 = T
| author-link2 = Tim Hubbard
| last3 = Fidelis
| first3 = K
| last4 = Pedersen
| first4 = J. T.
| issue = S3
| doi = 10.1002/(sici)1097-0134(1999)37:3+<2::aid-prot2>3.3.co;2-u
}}}}
| influences =
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| website = {{Plainlist|
- {{URL|https://kclpure.kcl.ac.uk/portal/tim.hubbard.html}}
- {{URL|https://www.sanger.ac.uk/external_person/hubbard-tim/}}}}
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}}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.{{twitter|name=Tim Hubbard}}{{Scopus|name=Hubbard, Tim J P}}{{ACMPortal|name=Tim J P Hubbard}}{{DBLP|name=Tim J. P. Hubbard}}{{cite news |last=Hopkin |first=Karen |date=2009-10-01 |title=Tim Hubbard: Genome Guru |url=http://www.the-scientist.com/?articles.view/articleNo/27686/title/Genome-Guru/ |newspaper=The Scientist |archive-date=2014-03-04 |archive-url=https://web.archive.org/web/20140304215812/http://www.the-scientist.com/?articles.view%2FarticleNo%2F27686%2Ftitle%2FGenome-Guru%2F |url-status=dead }}{{EuropePMC|ORCID=0000-0002-1767-9318}} From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.{{cite news |date=2023-12-01 | title=Tim Hubbard to be new ELIXIR Director |url=https://elixir-europe.org/news/new_director}}
Education
Hubbard was educated at the University of Cambridge where he was awarded a Bachelor of Arts degree in Natural Sciences (Biochemistry) in 1985. He went on to do research in protein design in the Department of Crystallography, Birkbeck College, London where he was awarded a PhD in 1988{{cite thesis |degree=PhD |first=Tim|last=Hubbard |title=The design, expression and characterisation of a novel protein |publisher=University of London |date=1988 |url=http://catalogue.senatehouselibrary.ac.uk/Record/b1582475|archive-url=https://web.archive.org/web/20150519132326/http://catalogue.senatehouselibrary.ac.uk/Record/b1582475|archive-date=2015-05-19}} for research supervised by Tom Blundell.
Research and career
Hubbard's research interests are in Bioinformatics, Computational biology and Genome Informatics. During his tenure at WTSI he supervised several successful PhD students to completion in these areas of research.{{cite thesis |degree=PhD |first=Markus|last=Brosch |title=Development of computational methods for analysing proteomic data for genome annotation |publisher=University of Cambridge |date=2010 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608690|oclc=890149364}}{{cite thesis |degree=PhD |first=Thomas Alexander|last=Down |title=Computational localization of promoters and transcription start sites in mammalian genomes |publisher=University of Cambridge |date=2004 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598623}}{{cite thesis |degree=PhD |first=Mutlu|last=Doğruel |title=Motif based computational identification of protein subcellular localisation |publisher=University of Cambridge |date=2008 |url=http://ulmss-newton.lib.cam.ac.uk/vwebv/holdingsInfo?bibId=30916|oclc=890154619}}{{cite thesis |degree=PhD |first=Jenny|last=Mattison |title=Analysis of genome-wide, cancer-associated mutation datasets in mouse and human |publisher=University of Cambridge |date=2009 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611118|oclc=890152898}}{{cite thesis |degree=PhD |first=Matias|last=Piipari |title=Inference and classification of eukaryotic cis-regulatory motifs |publisher=University of Cambridge |date=2011 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609801}}{{cite thesis |degree=PhD |first=Matthew Richard|last=Pocock |title=Computational analysis of genomes |publisher=University of Cambridge |date=2004 |url=http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615724|oclc=890159072}}
{{centered pull quote|Following a postdoctoral fellowship at the Protein Engineering Research Institute in Osaka under the EU scientific training program in Japan (1989-90) he returned to Cambridge becoming a Zeneca Fellow at the Medical Research Council (MRC), Centre for Protein Engineering. In 1997 he joined the Wellcome Trust Sanger Institute to become Head of Human Genome Analysis. Tim was Head of Informatics from 2007 to 2013, when he was seconded part time as specialist advisor to NHS England, involved in delivering genomics for health programmes.{{cite web|url=https://www.sanger.ac.uk/research/faculty/thubbard/|title=Wellcome Trust Sanger Institute Honorary Faculty - Dr Tim Hubbard|archive-url=https://web.archive.org/web/20150323181800/http://www.sanger.ac.uk/research/faculty/thubbard/|archive-date=2015-03-23}}}}
Hubbard was appointed Professor of Bioinformatics at King's in October 2013.{{cite web|url=https://kclpure.kcl.ac.uk/portal/tim.hubbard.html|title=Professor Tim Hubbard, King's College London|archive-url=https://web.archive.org/web/20140223072722/https://kclpure.kcl.ac.uk/portal/tim.hubbard.html|archive-date=2014-02-23}} His research has been published in leading peer reviewed scientific journals including Nature,{{Cite journal | author = ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET| doi = 10.1038/nature05874 | title = Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project | journal = Nature | volume = 447 | issue = 7146 | pages = 799–816 | year = 2007 | pmid = 17571346 | pmc =2212820 |bibcode = 2007Natur.447..799B |display-authors=etal}}{{Cite journal | first1 = E. S.
| last1 = Lander
| author-link1 = Eric Lander
| last2 = Linton | first2 = M.
| last3 = Birren | first3 = B.
| last4 = Nusbaum | first4 = C.
| last5 = Zody | first5 = C.
| last6 = Baldwin | first6 = J.
| last7 = Devon | first7 = K.
| last8 = Dewar | first8 = K.
| last9 = Doyle | first9 = M. | last10 = Fitzhugh | first10 = W. | last11 = Funke | first11 = R. | last12 = Gage | first12 = D. | last13 = Harris | first13 = K. | last14 = Heaford | first14 = A. | last15 = Howland | first15 = J. | last16 = Kann | first16 = L. | last17 = Lehoczky | first17 = J. | last18 = Levine | first18 = R. | last19 = McEwan | first19 = P. | last20 = McKernan | first20 = K. | last21 = Meldrim | first21 = J. | last22 = Mesirov | first22 = J. P. | last23 = Miranda | first23 = C. | last24 = Morris | first24 = W. | last25 = Naylor | first25 = J. | last26 = Raymond | first26 = C. | last27 = Rosetti | first27 = M. | last28 = Santos | first28 = R. | last29 = Sheridan | first29 = A. | last30 = Sougnez | first30 = C. | display-authors = 29
| title = Initial sequencing and analysis of the human genome
| journal = Nature
| volume = 409
| issue = 6822
| pages = 860–921
| date =Feb 2001
| issn = 0028-0836
| pmid = 11237011
| doi = 10.1038/35057062| url = https://deepblue.lib.umich.edu/bitstream/2027.42/62798/1/409860a0.pdf | bibcode = 2001Natur.409..860L| doi-access = free }}{{Cite journal
| pmid = 11236999
| pmc = 2658632
| year = 2001
| last1 = Birney
| first1 = E
| author-link1 = Ewan Birney
| title = Mining the draft human genome
| journal = Nature
| volume = 409
| issue = 6822
| pages = 827–8
| last2 = Bateman
| first2 = A
| author-link2 = Alex Bateman
| last3 = Clamp
| first3 = M. E.
| last4 = Hubbard
| first4 = T. J.
| author-link4 = Tim Hubbard
| doi = 10.1038/35057004
| bibcode = 2001Natur.409..827B
}} the Journal of Molecular Biology,{{Cite journal
| pmid = 9367767
| year = 1997
| last1 = Park
| first1 = J
| title = Intermediate sequences increase the detection of homology between sequences
| journal = Journal of Molecular Biology
| volume = 273
| issue = 1
| pages = 349–54
| last2 = Teichmann
| first2 = S. A.
| author-link2 = Sarah Teichmann
| last3 = Hubbard
| first3 = T
| author-link3 = Tim Hubbard
| last4 = Chothia
| first4 = C
| author-link4 = Cyrus Chothia
| doi = 10.1006/jmbi.1997.1288
}} Nucleic Acids Research, Genome Biology, Nature Methods,{{Cite journal | doi = 10.1038/nmeth.2722| title = Systematic evaluation of spliced alignment programs for RNA-seq data| journal = Nature Methods| volume = 10| issue = 12| pages = 1185–91| year = 2013| last1 = Engström | first1 = P. R. G. | last2 = Steijger | first2 = T. | last3 = Sipos | first3 = B. | last4 = Grant | first4 = G. R. | last5 = Kahles | first5 = A. | last6 = Alioto | first6 = T. | last7 = Behr | first7 = J. | last8 = Bertone | first8 = P. | last9 = Bohnert | first9 = R. | last10 = Campagna | first10 = D. | last11 = Davis | first11 = C. A. | last12 = Dobin | first12 = A. | last13 = Engström | first13 = P. R. G. | last14 = Gingeras | first14 = T. R. | last15 = Goldman | first15 = N. | last16 = Grant | first16 = G. R. | last17 = Guigó | first17 = R. | last18 = Harrow | first18 = J. | last19 = Hubbard | first19 = T. J. | last20 = Jean | first20 = G. R. | last21 = Kahles | first21 = A. | last22 = Kosarev | first22 = P. | last23 = Li | first23 = S. | last24 = Liu | first24 = J. | last25 = Mason | first25 = C. E. | last26 = Molodtsov | first26 = V. | last27 = Ning | first27 = Z. | last28 = Ponstingl | first28 = H. | last29 = Prins | first29 = J. F. | last30 = Rätsch | first30 = G. | pmid=24185836 | pmc=4018468}} Nature Reviews Cancer{{Cite journal
| pmid = 14993899
| pmc = 2665285
| year = 2004
| last1 = Futreal
| first1 = P. A.
| title = A census of human cancer genes
| journal = Nature Reviews Cancer
| volume = 4
| issue = 3
| pages = 177–83
| last2 = Coin
| first2 = L
| last3 = Marshall
| first3 = M
| last4 = Down
| first4 = T
| last5 = Hubbard
| first5 = T
| author-link5 = Tim Hubbard
| last6 = Wooster
| first6 = R
| last7 = Rahman
| first7 = N
| author-link7 = Nazneen Rahman
| last8 = Stratton
| first8 = M. R.
| author-link8 = Michael Stratton
| doi = 10.1038/nrc1299
}} and Bioinformatics.{{Cite journal | doi = 10.1093/bioinformatics/btn528| title = The Protein Feature Ontology: A tool for the unification of protein feature annotations| journal = Bioinformatics| volume = 24| issue = 23| pages = 2767–2772| year = 2008| last1 = Reeves | first1 = G. A.| last2 = Eilbeck | first2 = K.| last3 = Magrane | first3 = M.| last4 = O'Donovan | first4 = C.| last5 = Montecchi-Palazzi | first5 = L.| last6 = Harris | first6 = M. A.| last7 = Orchard | first7 = S.| last8 = Jimenez | first8 = R. C.| last9 = Prlic | first9 = A.| last10 = Hubbard | first10 = T. J. P.| author-link10= Tim Hubbard| last11 = Hermjakob | first11 = H.| last12 = Thornton | first12 = J. M.| author-link12 = Janet Thornton | pmid=18936051 | pmc=2912506}} His research been funded by the Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC).{{cite web|archive-url=https://web.archive.org/web/20150409093531/http://gtr.rcuk.ac.uk/person/A170197A-7ED0-4824-8F20-ABA7105D6D80|archive-date=2015-04-09|title=UK Government Grants awarded to Tim Hubbard|publisher=Research Councils UK|url=http://gtr.rcuk.ac.uk/person/A170197A-7ED0-4824-8F20-ABA7105D6D80}}
References
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{{DEFAULTSORT:Hubbard, Tim}}
Category:British bioinformaticians
Category:Alumni of Clare College, Cambridge