Dr Steve Searle

Dr Steve Searle's research involves generating and providing access to automatic annotation for genome sequences, in collaboration with the European Bioinformatics Institute.

Steve graduated from University of Bath in 1990 with BSc in Biochemistry and went on to complete his PhD in Molecular Modeling at the University, by modeling the structure of T cell receptors and antibodies and in 'humanising' them. After completing his PhD, Steve embarked on a postdoctoral fellowship at the University of Bath investigating MHC peptide interactions.

Before joining the Wellcome Trust Sanger Institute, Steve spent two years at the European Bioinformatics Institute (EBI) working in the group of Dr Geoff Barton on sequence and structural alignment algorithms and alignment assessment. During this time Steve was also involved in the development of the Apollo annotation browser/editor.

In 2001, Steve moved to the Ensembl Genebuild team at the Sanger Institute and became joint Head of the team in 2003. In 2009, Steve went on to become Joint Head of Vertebrate Annotation at the Institute. His teams are responsible for developing automatic gene annotation pipelines; generating Ensembl automatic gene annotation sets using those pipelines; and the development and maintenance of the Ensembl website.

Steve has been involved in many vertebrate genome consortia, providing gene annotation used in genome reference papers for organisms. Steve was also involved in analysis of human chromosome sequences during the Human Genome Project. He is involved in a number of major international collaborations, including the GENCODE annotation project for ENCODE project, collaborating with NCBI, UCSC and Havana to produce the CCDS annotation. Steve's interests range from improving automatic gene annotation pipelines, particularly by exploiting new data types and algorithms, to providing useful interfaces for presentation of Ensembl annotation on the Ensembl website.

Selected Publications

• Comparative and demographic analysis of orang-utan genomes.

  Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA and Wilson RK

  Nature 2011;469;7331;529-33

  PUBMED: 21270892; PMC: 3060778; DOI: 10.1038/nature09687

• Ensembl 2011.

  Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J and Searle SM

  Nucleic acids research 2011;39;Database issue;D800-6

  PUBMED: 21045057; PMC: 3013672; DOI: 10.1093/nar/gkq1064

• The genome of a songbird.

  Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER and Wilson RK

  Nature 2010;464;7289;757-62

  PUBMED: 20360741; PMC: 3187626; DOI: 10.1038/nature08819

• The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

  Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R and Lipman D

  Genome research 2009;19;7;1316-23

  PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108

• The Ensembl automatic gene annotation system.

  Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, Searle SM and Clamp M

  Genome research 2004;14;5;942-50

  PUBMED: 15123590; PMC: 479124; DOI: 10.1101/gr.1858004

• Apollo: a sequence annotation editor.

  Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ and Clamp ME

  Genome biology 2002;3;12;RESEARCH0082

  PUBMED: 12537571; PMC: 151184

Related links:

• Ensembl
• Vertebrate genome analysis