Research Biographies

DR COLIN SEMPLE

Biomedical Systems Analysis

Senior Investigator Scientist - Head of Bioinformatics

Contact Details

Research Areas

My interests are in using the huge volumes of genomic, transcriptomic and proteomic data to shed light on human evolution and disease. We carry out novel research in computational biology, often using comparative genomics to examine the molecular evolution of genes and genomes. Current projects include the evolution of noncoding DNA in primates and the role of the epigenomic landscape in human genome evolution. We also have long standing interests in computational candidate gene prioritization for disease or QTL mapping. However, we also collaborate with 'wet' lab biologists on diverse projects, from projects in cell and developmental biology to whole genome disease association studies.

Key/Selected Publications

• Semple, C.A. and Taylor, M.S. Molecular biology: The structure of change. Science 323:347-348, 2009 PubMed Abstract
• FANTOM Consortium: Suzuki, H.; Forrest, A.R.; van Nimwegen, E.; .....Semple, C.A.;....and Hayashizaki, Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41(5):553-562, 2009 PubMed Abstract
• Tenesa, A.; Farrington, S.M.; Prendergast, J.G.; Porteous, M.E.; Walker, M.; Haq, N.; Barnetson, R.A.; Theodoratou, E.; Cetnarskyj, R.; Cartwright, N.; Semple, C.; Clark, A.J.; Reid, F.J.; Smith, L.A.; Kavoussanakis, K.; Koessler, T.; Pharoah, P.D.; Buch, S.; Schafmayer, C.; Tepel, J.; Schreiber, S.; Volzke, H.; Schmidt, C.O.; Hampe, J.; Chang-Claude, J.; Hoffmeister, M.; Brenner, H.; Wilkening, S.; Canzian, F.; Capella, G.; Moreno, V.; Deary, I.J.; Starr, J.M.; Tomlinson, I.P.; Kemp, Z.; Howarth, K.; Carvajal-Carmona, L.; Webb, E.; Broderick, P.; Vijayakrishnan, J.; Houlston, R.S.; Rennert, G.; Ballinger, D.; Rozek, L.; Gruber, S.B.; Matsuda, K.; Kidokoro, T.; Nakamura, Y.; Zanke, B.W.; Greenwood, C.M.; Rangrej, J.; Kustra, R.; Montpetit, A.; Hudson, T.J.; Gallinger, S.; Campbell, H., and Dunlop, M.G. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.
  Nat Genet 40(5): 631-637, 2008
  PubMed Abstract
• Prendergast, J.G.; Campbell, H.; Gilbert, N.; Dunlop, M.G.; Bickmore, W.A. and Semple, C.A. Chromatin structure and evolution in the human genome. BMC Evol Biol 7:72, 2007
  PubMed Abstract
• Carninci, P.; Sandelin, A.; Lenhard, B.; Katayama, S.; Shimokawa, K.; Ponjavic, J.; Semple, C.A.; Taylor, M.S.; Engstrom, P.G.; Frith, M.C. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38:626-635, 2006 PubMed Abstract
• Taylor, M.S.; Kai, C.; Kawai, J.; Carninci, P.; Hayashizaki, Y. and Semple C.A. Heterotachy in mammalian promoter evolution. PLOS Genetics 2(4):e30, 2006 PubMed Abstracts
• Turner, F.S.; Clutterbuck, D.R.; Semple, C.A.M. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biology 4:R75, 2003 PubMed Abstract

Recent Publications

• Gyenesei A, Moody J, Semple CA, Haley CS, Wei WH: High-throughput analysis of epistasis in genome-wide association studies with BiForce. Bioinformatics 28:1957-1964, 2012.
  PubMed Abstract
• Nimmo ER, Prendergast JG, Aldhous MC, Kennedy NA, Henderson P, Drummond HE, Ramsahoye BH, Wilson DC, Semple CA, Satsangi J: Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway
  Inflamm Bowel Dis 18:889-899, 2012.
  PubMed Abstract
• Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ: Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages
  Proc Natl Acad Sci U S A 109:E944-E953, 2012.
  PubMed Abstract
• Prendergast JG, Semple CA: Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
  Genome Res 21:1777-1787, 2011.
  PubMed Abstract
• Semple F, MacPherson H, Webb S, Cox SL, Mallin LJ, Tyrrell C, Grimes GR, Semple CA, Nix MA, Millhauser GL, Dorin JR: Human beta-defensin 3 affects the activity of pro-inflammatory pathways associated with MyD88 and TRIF
  Eur J Immunol 41:3291-3300, 2011.
  PubMed Abstract
• White RE, Dickinson JR, Semple CA, Powell DJ, Berry C: The retroviral proteinase active site and the N-terminus of Ddi1 are required for repression of protein secretion. FEBS Lett 585:139-142, 2011. PubMed Abstract
• Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dolle P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A: A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9:e1000582, 2011. PubMed Abstract
• Andersen, K.M.; Madsen, L.; Prag, S.; Johnsen, A.H.; Semple, C.A.; Hendil, K.B. and Hartmann-Petersen, R. Thioredoxin Txnl1/TRP32 is a redox active co-factor of the 26S proteasome. Journal of Biological Chemistry, 284(22):15246-54, 2009 PubMed Abstract