Publication List


  1. Aitken S, Semple CA. 2017. The circadian dynamics of small nucleolar RNA in the mouse liver. J R Soc Interface, in press.
  2. Kaiser VB, Semple CA. 2017. When TADs go bad: chromatin structure and nuclear organisation in human disease. F1000Res, in press.
  3. Moore BL, Semple CA. 2017. Crossing borders: modeling approaches to understand chromatin domains and their boundaries. In ‘Epigenetics and Systems Biology’. Elsevier Inc, Cambridge MA, in press.
  4. Kaiser VB, Taylor MS, Semple CA. 2016. Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types. PLoS Genet 12: e1006207. PubMed Fulltext
  5. Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, Hayashizaki Y, Carninci P, Forrest AR; FANTOM Consortium, Semple CA, Dostie J, Pombo A, Nicodemi M. 2015. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol Syst Biol 11: 852. PubMed Fulltext
  6. Kaiser VB, Svinti V, Prendergast JG, Chau YY, Campbell A, Patarcic I, Barroso I, Joshi PK, Hastie ND, Miljkovic A, Taylor MS; Generation Scotland; UK10K, Enroth S, Memari Y, Kolb-Kokocinski A, Wright AF, Gyllensten U, Durbin R, Rudan I, Campbell H, Polašek O, Johansson Å, Sauer S, Porteous DJ, Fraser RM, Drake C, Vitart V, Hayward C, Semple CA, Wilson JF. 2015. Homozygous loss-of-function variants in European cosmopolitan and isolate populations. Hum Mol Genet 24: 5464-74. PubMed Fulltext
  7. Moore BL, Aitken S, Semple CA. 2015. Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization. Genome Biol 16: 110. PubMed Fulltext
  8. Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Khachigian LM, Okada-Hatakeyama M, Semple CA. 2015. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS Comput Biol 11: e1004217. PubMed Fulltext
  9. Prendergast JG, Chambers EV, Semple CA. 2014. Sequence level mechanisms of human epigenome evolution. Genome Biol Evol 6: 1758-71. PubMed Fulltext
  10. Wei WH, Guo Y, Kindt AS, Merriman TR, Semple CA, Wang K, Haley CS. 2014. Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid. Hum Mol Genet 23: 5061-8. PubMed Fulltext
  11. FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014. A promoter-level mammalian expression atlas. Nature 507: 462-70. PubMed Fulltext
  12. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. 2013. Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR. Genome Biol 14: R146. PubMed Fulltext
  13. Wei W, Gyenesei A, Semple CA, Haley CS. 2013. Properties of local interactions and their potential value in complementing genome-wide association studies. PLoS One 8: e71203. PubMed Fulltext
  14. Prendergast JG, Semple CA. 2013. Side effects: substantial non-neutral evolution flanking regulatory sites. PLoS Genet 9: e1003528. PubMed Fulltext
  15. Chambers EV, Bickmore WA, Semple CA. 2013. Divergence of mammalian higher order chromatin structure is associated with developmental loci. PLoS Comput Biol 9: e1003017. PubMed Fulltext
  16. Chambers EV, Semple CA. 2013. Chromatin structure and human genome evolution. In ‘Encyclopedia of Life Sciences’. John Wiley & Sons Ltd, London.
  17. Kindt AS, Navarro P, Semple CA, Haley CS. 2013. The genomic signature of trait-associated variants. BMC Genomics 14: 108. PubMed Fulltext
  18. Dunlop MG et al. 2012. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nature Genet 44: 770-776. PubMed Fulltext
  19. Gyenesei A, Moody J, Semple CA, Haley CS, Wei W-H. 2012. High throughput analysis of epistasis in genome-wide association studies with BiForce. Bioinformatics 28: 1957-64. PubMed Fulltext
  20. Gyenesei A, Moody J, Laiho A, Semple CA, Haley CS, Wei W-H. 2012. BiForce Toolbox: Powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies. Nucleic Acids Res 40: W628-32. PubMed Fulltext
  21. Prendergast JG, Tong P, Hay DC, Farrington SM, Semple CA. 2012. A genome-wide screen for allele specific histone modifications in human embryonic stem cells reveals novel sites associated with known disease loci. Epigenetics and Chromatin 5: 6. PubMed Fulltext
  22. Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao K-A, Masterman K-A, 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. 2012. 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: E944-53. PubMed Fulltext
  23. Nimmo ER, Prendergast JG, Aldhous MC, Kennedy NA, Drummond HE, Ramsahoye BH, Wilson DC, Semple CA, Satsangi J. 2012. 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: 889-99. PubMed Fulltext
  24. Chambers EV, Kindt AS, Semple CA. 2011. Opening sequence: computational genomics in the era of high-throughput sequencing. Genome Biol 12: 310. PubMed Fulltext
  25. Prendergast JG, Semple CA. 2011. Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res 21: 1777-87. PubMed Fulltext
  26. Semple F, Macpherson H, Webb S, Cox SL, Mallin LJ, Tyrrell C, Grimes GR, Semple CA, Nix MA, Millhauser GL, Dorin JR. 2011. Human beta-defensin 3 affects the activity of pro-inflammatory pathways associated with MyD88 and TRIF. Eur J Immunol 41: 3291-300. PubMed Fulltext
  27. 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, Nürnberger 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, Dollé P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A. 2011 A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo. PLoS Biol 9: e1000582. PubMed Fulltext
  28. White RE, Dickinson JR, Semple CA, Powell DJ, Berry C. 2010. The retroviral proteinase active site and the N-terminus of Ddi1 are required for repression of protein secretion. FEBS Lett 585: 139-42. PubMed
  29. Taylor MS, Jordan G, Semple CA. 2010. Comparative genomics and mammalian promoter evolution. In ‘Cap-analysis gene expression (CAGE): The Science of Decoding Gene Transcription’ (Edited by Piero Carninci).
  30. Madsen L, Seeger M, Semple CA, Hartmann-Petersen R. 2009. New ATPase regulators-p97 goes to the PUB. Int J Biochem Cell Biol 41: 2380-8. PubMed
  31. Andersen KM, Madsen L, Prag S, Johnsen AH, Semple CA, Hendil KB, Hartmann-Petersen R. 2009. Thioredoxin Txnl1/TRP32 is a redox active co-factor of the 26S proteasome. J Biol Chem 284: 15246-54. PubMed
  32. The FANTOM Consortium. 2009. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562. PubMed
  33. Semple CA, Taylor MS. 2009. Molecular biology: The structure of change. Science 323: 347-348. PubMed
  34. Michlewski G, Guil S, Semple CA, Caceres JF. 2008. Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol Cell 32: 383-393. PubMed
  35. Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. 2008. Rapidly evolving human promoter regions. Nat Genet 40: 1262-1263. PubMed
  36. Madsen L, Andersen KM, Prag S, Moos T, Semple CA, Seeger M, Hartmann-Petersen R. 2008. Ubxd1 is a novel co-factor of the human p97 ATPase. Int J Biochem Cell Biol 40:2927-42. PubMed
  37. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N, Barnetson RA, Theodoratou E, Cetnarskyj R, Cartwright N, Semple C, Clark AJ, Reid FJ, Smith LA, Kavoussanakis K, Koessler T, Pharoah PD, Buch S, Schafmayer C, Tepel J, Schreiber S, Völzke H, Schmidt CO, Hampe J, Chang-Claude J, Hoffmeister M, Brenner H, Wilkening S, Canzian F, Capella G, Moreno V, Deary IJ, Starr JM, Tomlinson IP, Kemp Z, Carvajal-Carmona L, Webb E, Broderick P, Vijayakrishnan J, Houlston RS, Rennert G, Ballinger D, Rozek L, Gruber SB, Matsuda K, Kidokoro T, Nakamura Y, Zanke BW, Greenwood CM, Rangrej J, Kustra R, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG. 2008. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.Nat Genet 40:631-637. PubMed
  38. Semple CA. 2008. Chromatin structure and human genome evolution. In ‘Encyclopedia of Life Sciences’. John Wiley & Sons Ltd, London.
  39. Prendergast JG, Campbell H, Gilbert N, Dunlop MG, Bickmore WA, Semple CA. 2007. Chromatin structure and evolution in the human genome. BMC Evol Biol 7: 72. PubMed
  40. Semple, CAM. 2007. Assembling a view of the human genome. In ‘Bioinformatics for Geneticists’ 2nd edition (Edited by Barnes MR). John Wiley & Sons Ltd, London.
  41. Andersen KM, Semple CA, Hartmann-Petersen R. 2007. Characterisation of the nascent polypeptide-associated complex in fission yeast. Mol Biol Rep 34: 275-81. PubMed
  42. Semple CA, Gautier G, Taylor K, Dorin JR. 2006. The changing of the guard: molecular diversity and rapid evolution of beta-defensins. Mol Divers 10: 575-84. PubMed
  43. Sutherland HG, Newton K, Brownstein DG, Holmes MC, Kress C, Semple CA, Bickmore WA. 2006. Disruption of Ledgf/Psip1 results in perinatal mortality and homeotic skeletal transformations. Mol Cell Biol 26: 7201-10. PubMed
  44. Crow YJ, Leitch A, Hayward BE, Garner A, Parmar R, Griffith E, Ali M, Semple C, Aicardi J, Babul-Hirji R, Baumann C, Baxter P, Bertini E, Chandler KE, Chitayat D, Cau D, Dery C, Fazzi E, Goizet C, King MD, Klepper J, Lacombe D, Lanzi G, Lyall H, Martinez-Frias ML, Mathieu M, McKeown C, Monier A, Oade Y, Quarrell OW, Rittey CD, Rogers RC, Sanchis A, Stephenson JB, Tacke U, Till M, Tolmie JL, Tomlin P, Voit T, Weschke B, Woods CG, Lebon P, Bonthron DT, Ponting CP, Jackson AP. 2006. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. Nat Genet 38: 910-6. PubMed
  45. Costa Y, Speed RM, Gautier P, Semple CA, Maratou K, Turner JM, Cooke HJ. 2006. Mouse MAELSTROM – The link between Meiotic Silencing of Unsynapsed Chromatin and microRNA pathway? Hum Mol Genet: 15: 2324-34. PubMed
  46. Tiffin N, Adie E, Turner F, Brunner H, van Driel M, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro M, Adeyemo A, Patti M, Semple CA, Hide W. 2006.  Computational disease gene identification: a concert of methods prioritises type 2 diabetes and obesity candidate genes. Nucleic Acids Res 34: 3067-81. PubMed
  47. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC et al. 2006. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635. PubMed
  48. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA. 2006. Heterotachy in mammalian promoter evolution. PLOS Genet 2(4): e30. PubMed
  49. Semple CA, Taylor K, Eastwood H, Barran PE, Dorin JR. 2006. Beta-defensin evolution: selection complexity and clues for residues of functional importance. Biochem Soc Trans, 34: 257-62. PubMed
  50. Reynolds N, Collier B, Bingham V, Maratou K, Speed RM, Taggart M, Semple CA, Gray, NK, Cooke HJ. 2005. Dazl controls the translation of specific transcripts required for gametogenesis in the mammalian germline. Hum Mol Genet 14: 3899-3909. PubMed
  51. The FANTOM Consortium. 2005. The Transcriptional Landscape of the Mammalian Genome. Science 309: 1559-1563. PubMed
  52. Costa Y, Speed R, Ollinger R, Alsheimer M, Semple CA, Gautier P, Maratou K, Novak I, Hoog C, Benavente R, Cooke HJ. 2005. Two novel proteins recruited by SYCP1 are at the centre of meiosis. J Cell Sci 118: 2755-62. PubMed
  53. Clutterbuck DR, Leroy A, O Connell MA, Semple CAM. 2005. A Bioinformatic Screen for Novel A-I RNA Editing Sites Reveals Re-Coding Editing in BC10. Bioinformatics 21: 2590. PubMed
  54. Semple CA, Maxwell A, Gautier P, Kilanowski FM, Eastwood H, Barran PE, Dorin JR. 2005. The complexity of selection at the major primate beta-defensin locus. BMC Evol Biol 5: 32. PubMed
  55. Semple CAM. 2004. Deep genomics in shallow times: the finished sequence of human chromosomes 13 and 19. Eur J Hum Genet 12: 875-876. PubMed
  56. Turner FS, Clutterbuck DR, Semple CAM. 2003. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol 4: R75. PubMed
  57. Semple CAM. 2003. Meet the parents: bioinformatics and computational biology. Heredity 91: 542-3. (A book review of ‘Frontiers in Computational Genomics’ edited by Galperin and Koonin.) Fulltext
  58. Semple CAM. 2003. The comparative proteomics of ubiquitination in mouse. Genome Res 13: 1389-1394. PubMed
  59. Semple CAM, Rolfe M, Dorin JR. 2003. Duplication and selection in the evolution of primate beta-defensin genes. Genome Biol 4(5): R31. PubMed
  60. Morrison GM, Semple CAM, Kilanowski F, Hill RE, Dorin JR. 2003.  Evidence of adaptive evolution after gene duplication in the murine beta-defensin gene family. Mol Biol Evol 20: 460-470. PubMed
  61. Hartmann-Petersen R, Semple CA, Ponting CP, Hendil KB, Gordon C. 2003. UBA domain containing proteins in fission yeast. Int J Biochem Cell Biol 35: 629-36. PubMed
  62. Semple, CAM. 2003. Assembling a view of the human genome. In ‘Bioinformatics for Geneticists’ (Edited by Barnes MR and Gray IC). John Wiley & Sons Ltd, London.
  63. The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team. 2002. Analysis of the mouse transcriptome based upon functional annotation of 60,770 full length cDNAs. Nature 420: 563-573. PubMed
  64. Taylor, MS, Semple CAM. 2002. Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes. Genome Biol 3(9): reviews1025.1-1025.6. PubMed
  65. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CAM, Blackwood DHR, Porteous DJ, Evans KL. 2002. SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res, 30: e74. PubMed
  66. Semple CAM, Morris SW, Porteous DJ, Evans KL. 2002. Computational comparison of human genomic sequence assemblies for a region of chromosome 4. Genome Res 12: 424-429. PubMed
  67. Wilkinson CRM, Seeger M, Hartmann-Petersen R, Stone M, Wallace M, Semple C, Gordon C. 2001. Proteins containing the UBA domain are able to bind to multi-ubiquitin chains. Nat Cell Biol 3: 939-943. PubMed
  68. Le Hellard S, Semple CAM, Morris SW, Evans KL, Porteous DJ. 2001. Physical mapping: Integrating computational and molecular genetic data. Ann Human Genet 65: 221-228. PubMed
  69. Semple CAM. 2001. Bases and spaces: resources on the web for accessing the draft human genome – II – After publication of the draft. Genome Biol 2(6): reviews2001.1-2001.6. PubMed
  70. Semple CAM, Evans KL, Porteous DJ. 2001. Twin peaks: The draft human genome sequence. Genome Biol 2(3): comment2003.1-2003.5. PubMed
  71. Devon RS, Anderson S, Teague PW, Burgess P, Kipari TMJ, Semple CAM, Millar JK, Muir WJ, Murray V, Pelosi AJ, Blackwood DHR, Porteous DJ. 2001. Identification of polymorphisms within Disrupted in Schizophrenia 1 and 2, and an investigation of their association with schizophrenia and bipolar disorder. Psychiatr Genet, 11: 71-78. PubMed
  72. Semple CAM, Devon RS, Le Hellard S, Porteous DJ. 2001. Identification of genes from a schizophrenia-linked translocation breakpoint region. Genomics: 73: 123-126. PubMed
  73. Evans KL, Le Hellard S, Morris SW, Lawson D, Whitton C, Semple CAM, Malloy MP, Maule JC, Gregory SS, Ross MT, Bentley DR, Blackwood DHR, Porteous DJ. 2001. A 6Mb Contig of a region of human chromosome 4p that is linked to Bipolar Affective Disorder. Genomics: 71: 315-323. PubMed
  74. Shouse B. 2001. HUMAN GENOME: Less Can Be More, U.K. Study Finds. Science 293: 1238-1239. (A report on a talk I gave at the CSHL/Wellcome Trust Genome Informatics conference, Aug 2001.) PubMed
  75. Semple CAM, Evans KL, Morris SW, Porteous DJ. 2001. Letter: Comparing Human Genome Mapping Data. Science 293: 2394-2395. (Corrections to the report by B. Shouse above.) PubMed
  76. Semple CAM, Taylor MS, Ballereau S. 2001. The meso-genomic era. Genome Biol 2(7): reports4015.1-4015.5. PubMed
  77. Semple, C. 2000. Bases and spaces: resources on the web for accessing the draft human genome. Genome Biol 1(4): reviews2001.1-2001.5. PubMed
  78. Semple CAM, Morris SW, Porteous DJ and Evans KL. 2000. In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder. Bioinformatics 16: 735-738. PubMed
  79. Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS, Semple CAM, Devon RS, St Clair DM, Muir WJ, Blackwood DHR, Porteous DJ. 2000. Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum Mol Genet 9: 1415-1423. PubMed
  80. Semple C. 2000. Gene Prediction: The end of the beginning. Genome Biol 1(2): reports4012.1-4012.3. Fulltext
  81. Millar JK, Christie C, Semple CAM, Porteous DJ. 2000. Chromosomal location and genomic structure of the human translin-associated factor X gene (TRAX; TSNAX) revealed by intergenic splicing to DISC1, a gene disrupted by a translocation segregating with schizophrenia. Genomics 67: 69-77. PubMed
  82. Semple C, Wolfe KH. 1999. Gene duplication and gene conversion in the C. elegans genome. J Mol Evol 48:  555-564. PubMed
  83. Fowler K, Semple C, Barton NH, Partridge L. 1997. Genetic variation for total fitness in D. melanogaster. Proceedings of the Royal Society of London, Series B. 264: 1379, 191-199. PubMed