Tim Hubbard

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.^{[7][8][9][10][11][12][13]} From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.^[14]

Tim Hubbard
Born	Timothy John Phillip Hubbard
Alma mater	University of Cambridge (BA) Birkbeck College, London (PhD)
Known for	SCOP database[1] GENCODE[2] Ensembl[3][4] CASP[5]
Scientific career
Fields	Bioinformatics Computational Biology Genome Informatics[6]
Institutions	King's College London Genomics England[7] NHS England Wellcome Trust Sanger Institute
Thesis	The design, expression and characterisation of a novel protein (1988)
Doctoral advisor	Tom Blundell
Website	kclpure.kcl.ac.uk/portal/tim.hubbard.html www.sanger.ac.uk/external_person/hubbard-tim/

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^[15] for research supervised by Tom Blundell.

Research and career

Hubbard's research interests are in Bioinformatics, Computational biology and Genome Informatics.^[6] During his tenure at WTSI he supervised several successful PhD students to completion in these areas of research.^{[16][17][18][19][20][21]}

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.^[22]

Hubbard was appointed Professor of Bioinformatics at King's in October 2013.^[23] His research has been published in leading peer reviewed scientific journals including Nature,^[24][25][26] the Journal of Molecular Biology,^[1][27] Nucleic Acids Research,^[3][4] Genome Biology,^[2] Nature Methods,^[28] Nature Reviews Cancer^[29] and Bioinformatics.^[30] His research been funded by the Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC).^[31]

References

1. Murzin, A. G.; Brenner, S.; Hubbard, T.; Chothia, C. (1995). "SCOP: A structural classification of proteins database for the investigation of sequences and structures" (PDF). Journal of Molecular Biology. 247 (4): 536–540. doi:10.1016/S0022-2836(05)80134-2. PMID 7723011. Archived from the original (PDF) on 2012-04-26.
2. Harrow, J; Denoeud, F; Frankish, A; Reymond, A; Chen, C. K.; Chrast, J; Lagarde, J; Gilbert, J. G.; Storey, R; Swarbreck, D; Rossier, C; Ucla, C; Hubbard, T; Antonarakis, S. E.; Guigo, R (2006). "GENCODE: Producing a reference annotation for ENCODE". Genome Biology. 7 (Suppl 1): S4.1–9. doi:10.1186/gb-2006-7-s1-s4. PMC 1810553. PMID 16925838.
3. Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research. 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. PMID 11752248.
4. Farrell, C. M.; O'Leary, N. A.; Harte, R. A.; Loveland, J. E.; Wilming, L. G.; Wallin, C.; Diekhans, M.; Barrell, D.; Searle, S. M. J.; Aken, B.; Hiatt, S. M.; Frankish, A.; Suner, M. -M.; Rajput, B.; Steward, C. A.; Brown, G. R.; Bennett, R.; Murphy, M.; Wu, W.; Kay, M. P.; Hart, J.; Rajan, J.; Weber, J.; Snow, C.; Riddick, L. D.; Hunt, T.; Webb, D.; Thomas, M.; Tamez, P.; Rangwala, S. H. (2013). "Current status and new features of the Consensus Coding Sequence database". Nucleic Acids Research. 42 (Database issue): D865–D872. doi:10.1093/nar/gkt1059. PMC 3965069. PMID 24217909.
5. Moult, J; Hubbard, T; Fidelis, K; Pedersen, J. T. (1999). "Critical assessment of methods of protein structure prediction (CASP): Round III". Proteins. Suppl 3 (S3): 2–6. doi:10.1002/(sici)1097-0134(1999)37:3+<2::aid-prot2>3.3.co;2-u. PMID 10526346.
6. Tim Hubbard publications indexed by Google Scholar
7. "Genomics England publishes results of its annotation assessment". Genomics England. 2014. Archived from the original on 2015-01-12.
8. Tim Hubbard on Twitter
9. Hubbard, Tim J P's publications indexed by the Scopus bibliographic database. (subscription required)
10. Tim J P Hubbard author profile page at the ACM Digital Library
11. Tim J. P. Hubbard at DBLP Bibliography Server
12. Hopkin, Karen (2009-10-01). "Tim Hubbard: Genome Guru". The Scientist. Archived from the original on 2014-03-04.
13. Tim Hubbard publications from Europe PubMed Central
14. "Tim Hubbard to be new ELIXIR Director". 2023-12-01.
15. Hubbard, Tim (1988). The design, expression and characterisation of a novel protein (PhD thesis). University of London. Archived from the original on 2015-05-19.
16. Brosch, Markus (2010). Development of computational methods for analysing proteomic data for genome annotation (PhD thesis). University of Cambridge. OCLC 890149364.
17. Down, Thomas Alexander (2004). Computational localization of promoters and transcription start sites in mammalian genomes (PhD thesis). University of Cambridge.
18. Doğruel, Mutlu (2008). Motif based computational identification of protein subcellular localisation (PhD thesis). University of Cambridge. OCLC 890154619.
19. Mattison, Jenny (2009). Analysis of genome-wide, cancer-associated mutation datasets in mouse and human (PhD thesis). University of Cambridge. OCLC 890152898.
20. Piipari, Matias (2011). Inference and classification of eukaryotic cis-regulatory motifs (PhD thesis). University of Cambridge.
21. Pocock, Matthew Richard (2004). Computational analysis of genomes (PhD thesis). University of Cambridge. OCLC 890159072.
22. "Wellcome Trust Sanger Institute Honorary Faculty - Dr Tim Hubbard". Archived from the original on 2015-03-23.
23. "Professor Tim Hubbard, King's College London". Archived from the original on 2014-02-23.
24. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET; et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.{{cite journal}}: CS1 maint: multiple names: authors list (link)
25. Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011.
26. Birney, E; Bateman, A; Clamp, M. E.; Hubbard, T. J. (2001). "Mining the draft human genome". Nature. 409 (6822): 827–8. Bibcode:2001Natur.409..827B. doi:10.1038/35057004. PMC 2658632. PMID 11236999.
27. Park, J; Teichmann, S. A.; Hubbard, T; Chothia, C (1997). "Intermediate sequences increase the detection of homology between sequences". Journal of Molecular Biology. 273 (1): 349–54. doi:10.1006/jmbi.1997.1288. PMID 9367767.
28. Engström, P. R. G.; Steijger, T.; Sipos, B.; Grant, G. R.; Kahles, A.; Alioto, T.; Behr, J.; Bertone, P.; Bohnert, R.; Campagna, D.; Davis, C. A.; Dobin, A.; Engström, P. R. G.; Gingeras, T. R.; Goldman, N.; Grant, G. R.; Guigó, R.; Harrow, J.; Hubbard, T. J.; Jean, G. R.; Kahles, A.; Kosarev, P.; Li, S.; Liu, J.; Mason, C. E.; Molodtsov, V.; Ning, Z.; Ponstingl, H.; Prins, J. F.; Rätsch, G. (2013). "Systematic evaluation of spliced alignment programs for RNA-seq data". Nature Methods. 10 (12): 1185–91. doi:10.1038/nmeth.2722. PMC 4018468. PMID 24185836.
29. Futreal, P. A.; Coin, L; Marshall, M; Down, T; Hubbard, T; Wooster, R; Rahman, N; Stratton, M. R. (2004). "A census of human cancer genes". Nature Reviews Cancer. 4 (3): 177–83. doi:10.1038/nrc1299. PMC 2665285. PMID 14993899.
30. Reeves, G. A.; Eilbeck, K.; Magrane, M.; O'Donovan, C.; Montecchi-Palazzi, L.; Harris, M. A.; Orchard, S.; Jimenez, R. C.; Prlic, A.; Hubbard, T. J. P.; Hermjakob, H.; Thornton, J. M. (2008). "The Protein Feature Ontology: A tool for the unification of protein feature annotations". Bioinformatics. 24 (23): 2767–2772. doi:10.1093/bioinformatics/btn528. PMC 2912506. PMID 18936051.
31. "UK Government Grants awarded to Tim Hubbard". Research Councils UK. Archived from the original on 2015-04-09.