Archive Page: Professor Tim Hubbard

Archive Page: Professor Tim Hubbard

Archive Page - this page is maintained as a historical record and is no longer being updated

Please note: This page is no longer being updated and was last edited in 2013.

From 1996 to 2013, Professor Hubbard worked at the Sanger Institute, first on the Human Genome Project and then leading the Vertebrate Genome Analysis Project, which generates and presents core vertebrate genome annotation and maintains the reference genome sequences.

Tim is Professor of Bioinformatics, Head of Department of Medical and Molecular Genetics at King's College London and overall Director of Bioinformatics for King's Health Partners/King's College London. Tim also has a part-time appointment as Head of Bioinformatics at Genomics England, the company set up by the Government to help deliver the 100k Genome Project.

From 1996 to 2013, Professor Hubbard worked at the Sanger Institute, first on the Human Genome Project and then leading the Vertebrate Genome Analysis Project, which generates and presents core vertebrate genome annotation and maintains the reference genome sequences.

Tim graduated with a BA in Biochemistry from University of Cambridge in 1985 and a PhD in Protein Design from the Department of Crystallography, Birkbeck College, London in 1988.

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.

Before joining the Sanger Institute Tim worked mainly on protein folding, classification and design. In 1994 he co-founded SCOP ( the Structural Classification of Proteins database ) , thought to be the first biological database designed from the start to take advantage of the then new World Wide Web. He developed algorithms to make protein structure predictions and assess their accuracy and to calibrate the reliability of sequence alignment methods. He was one of the most successful participants in the first CASP ( Critical Assessment of Structure Prediction ) competition in 1994 and a co-organiser of subsequent CASP competitions ( CASP2-CASP7 ) until 2007.

At the Sanger Institute Tim was a member of the strategy group that organised the sequencing of the human genome as part of the international public consortium. During this time he built up groups to analyse and annotate the sequences of vertebrate genomes. In 1999 he developed an automatic annotation system and starting applying it in real time to sequence output of the human genome project. This evolved into the Ensembl project with Michele Clamp and Ewan Birney from the European Bioinformatics Institute ( EBI ) , which now provides annotation to more than 40 genomes. In parallel, the HAVANA group have carried out large scale manual annotation of human, mouse and zebrafish genomes. Since 2007 Tim has been the principal investigator of GENCODE, a scale up programme of the ENCODE project, which brings together HAVANA, Ensembl and seven external groups to generate the reference geneset for the human genome. He was also the Sanger Institute principal investigator of the Genome Reference Consortium, which is responsible for reference genome sequences of human, mouse and zebrafish.

Tim also ran a research group that used machine learning approaches to develop ab initio algorithms for vertebrate genome annotation such as large scale motif discovery. The group also developed components of bioinformatics infrastructure, including the popular biojava open source Java framework for processing biological data was ( started in the group in 1997 ) and components of the Distributed Annotation System ( DAS ) including the SPICE DAS client, the Dazzle DAS Server and the DAS registry.

Tim has served on many national and international advisory boards including the advisory council of the RIKEN Genome Science Centre, Japan as chairman ( 2005-2007 ) , the advisory board of ukPMC ( UK PubMedCentral ) as deputy chair ( 2007- ) , the E-Health Records Research Board of the UK Government Office for Strategic Coordination of Health Research ( OSCHR ) ( 2007-2009 ) which was the external reference group for NHS Research Capability Programme ( RCP ) and the Bioinformatics and Education, Engagement & Training Working Groups of the UK Department of Health Human Genomics Strategy Group ( HGSG ) ( 2010- ) setup in response to the 2009 House of Lords Science and Technology Committee Report on Genomic Medicine. In his private capacity he is also significantly involved in international policy discussions around innovation, intellectual property and public health.

Selected Publications

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR,Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S,Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ,Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H,Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM,Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ,Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P,Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL,Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A,Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC,Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS,Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J,Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X,Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J,Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED,Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S,Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B,Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute,Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD,Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ,Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J,Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN,Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS,Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G,Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD,Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC,Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B,McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK,Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B and de Jong PJ. Nature 2007;447;7146;799-816. PUBMED: 17571346; PMC: 2212820; DOI: 10.1038/nature05874

Large-scale discovery of promoter motifs in Drosophila melanogaster. Down TA, Bergman CM, Su J and Hubbard TJ. PLoS computational biology 2007;3;1;e7. PUBMED: 17238282; PMC: 1779301; DOI: 10.1371/journal.pcbi.0030007

Integrating sequence and structural biology with DAS. Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A and Hubbard TJ. BMC bioinformatics 2007;8;333. PUBMED: 17850653; PMC: 2031907; DOI: 10.1186/1471-2105-8-333

GENCODE: producing a reference annotation for ENCODE. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R,Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE and Guigo R. Genome biology 2006;7 Suppl 1;S4.1-9. PUBMED: 16925838; PMC: 1810553; DOI: 10.1186/gb-2006-7-s1-s4

Initial sequencing and comparative analysis of the mouse genome. Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J,Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N,Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S,Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR,Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR,Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN,Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L,Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D,Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A,Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D,Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS,Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR,McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL,Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO,Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E,Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC,Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R,Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S,Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B,Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D,Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M,Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J,Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM,Zody MC and Lander ES. Nature 2002;420;6915;520-62. PUBMED: 12466850; DOI: 10.1038/nature01262

The Ensembl genome database project. 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, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I and Clamp M. Nucleic acids research 2002;30;1;38-41. PUBMED: 11752248; PMC: 99161

Initial sequencing and analysis of the human genome. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, 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 JP, Miranda C, Morris W, Naylor J, Raymond C,Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A,Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N,Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D,Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR,Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS,Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S,Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA,Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML,Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T,Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W,Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L,Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S,Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW,Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR,Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M,Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA,Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D,Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C,Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S,Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM,McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J,Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J,Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J,Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K,Shizuya H, Choi S, Chen YJ, Szustakowki J and International Human Genome Sequencing Consortium. Nature 2001;409;6822;860-921. PUBMED: 11237011; DOI: 10.1038/35057062

RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Hubbard TJ. Proteins 1999;Suppl 3;15-21. PUBMED: 10526348

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Brenner SE, Chothia C and Hubbard TJ. Proceedings of the National Academy of Sciences of the United States of America 1998;95;11;6073-8. PUBMED: 9600919; PMC: 27587

SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin AG, Brenner SE, Hubbard T and Chothia C. Journal of molecular biology 1995;247;4;536-40. PUBMED: 7723011; DOI: 10.1006/jmbi.1995.0159