Full Publications

  1. Aitken S, Firth HV, Wright CF, Hurles ME, FitzPatrick DR, Semple CA. 2022. IMPROVE-DD: Integrating Multiple Phenotype Resources Optimises Variant Evaluation in genetically determined Developmental Disorders. HGG Advances S2666-2477(22)00079-3 Fulltext
  2. Hollis RL, Meynert AM, Michie CO, Rye T, Churchman M, Hallas-Potts A, Croy I, McCluggage WG, Williams ARW, Bartos C, Iida Y, Okamoto A, Dougherty B, Barrett JC, March R, Matakidou A, Roxburgh P, Semple CA, Harkin DP, Kennedy R, Herrington CS, Gourley C. 2022. Multiomic characterisation of high grade serous ovarian carcinoma enables high resolution patient stratification. Clin Cancer Res 28: 3546-3556. PubMed Fulltext
  3. Blackmur JP, Vaughan-Shaw PG, Donnelly K, Harris BT, Svinti V, Ochocka-Fox AM, Freile P, Walker M, Gurran T, Reid S, Semple CA, Din FVN, Timofeeva M, Dunlop MG, Farrington SM. 2022. Gene Co-Expression Network Analysis Identifies Vitamin D-Associated Gene Modules in Adult Normal Rectal Epithelium Following Supplementation. Front Genet 12: 783970. PubMed Fulltext
  4. Bolado-Carrancio A, Lee M, Ewing A, Muir M, Macleod KG, Gallagher WM, Nguyen LK, Carragher NO, Semple CA, Brunton VG, Caswell PT, von Kriegsheim A. 2021. ISGylation drives basal breast tumour progression by promoting EGFR recycling and Akt signalling. Oncogene 40: 6235-6247. PubMed Fulltext
  5. Kaiser VB, Talmane L, Kumar Y, Semple F, MacLennan M, Deciphering Developmental Disorders Study, FitzPatrick DR, Taylor MS, Semple CA. 2021. Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome. Genome Res 31: 1-14. PubMed Fulltext
  6. Hollis RL, Thomson JP, Stanley B, Churchman M, Meynert AM, Rye T, Bartos C, Croy I, Mackean M, Nussey F, Semple CA, Gourley C, Herrington CS. 2021. Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification. NPJ Precis Oncol 5: 47. PubMed Fulltext
  7. Ewing A, Meynert A, Churchman M, Grimes GR, Hollis RL, Herrington CS, Rye T, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Dowson S, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D, McMahon L, Matakidou A, Dougherty B, March R, Barrett JC, McNeish IA, Scottish Genomes Partnership, Biankin AV, Roxburgh P, Gourley C, Semple CA. 2021. Structural variants at the BRCA1/2 loci are a common source of homologous repair deficiency in high grade serous ovarian carcinoma. Clin Cancer Res: 27: 3201-3214. PubMed Fulltext
  8. Bonneau M, Sullivan STO, Gonzalez-Lozano MA, Baxter P, Gautier P, Marchisella E, Hardingham NR, Chesters RA, Torrance H, Howard DM, Jansen MA, McMillan M, Singh Y, Didier M, Koopmans F, Semple CA, McIntosh AM, Volkmer H, Loos M, Fox K, Hardingham GE, Vernon AC, Porteous DJ, Smit AB, Price DJ, Kirsty Millar J. 2021. Functional brain defects in a mouse model of a chromosomal t(1;11) translocation that disrupts DISC1 and confers increased risk of psychiatric illness. Transl Psychiatry 11: 135. PubMed Fulltext
  9. Parry DA, Tamayo-Orrego L, Carroll P, Marsh JA, Greene P, Murina O, Uggenti C, Leitch A; Scottish Genomes Partnership, Káposzta R, Merő G, Nagy A, Orlik B, Kovács-Pászthy B, Quigley AJ, Riszter M, Rankin J, Reijns MAM, Szakszon K, Jackson AP. 2020. PRIM1 deficiency causes a distinctive primordial dwarfism syndrome. Genes Dev 34: 1520-33. PubMed Fulltext
  10. Hollis R, Thomson JP, Stanley B, Churchman M, Meynert A, Rye T, Bartos C, Iida Y, Croy I, Mackean M, Nussey F, Okamoto A, Semple CA, Gourley C, Herrington CS. 2020. Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome. Nat Commun 11: 4995. PubMed Fulltext
  11. Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. 2020. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 30: 1060-1072. PubMed Fulltext
  12. Aitken SA, Anderson CJ, Connor F, Pich O, Sundaram V, Feig C, Rayner TF, Lukk M, Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes S, Davies SE, Drews RM, Ewing A, Kaiser VB, Khamseh A, López-Arribillaga E, Redmond AM, Santoyo-Lopez J, Sentís I, Talmane L, Yates AD, Semple CA, López- Bigas N, Flicek P, Odom DT, Taylor MS. 2020. Pervasive lesion segregation shapes cancer genome evolution. Nature 583: 265-270. PubMed Fulltext
  13. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. 2020. Pan-cancer analysis of whole genomes. Nature 578: 82-93. PubMed Fulltext
  14. Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L; S. G. P. Consortium, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF. 2019. Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions. PLoS Genet 15: e1008480. PubMed Fulltext
  15. Travnickova J, Wojciechowska S, Khamseh A, Gautier P, Brown DV, Lefevre T, Brombin A, Ewing A, Capper A, Spitzer M, Dilshat R, Semple CA, Mathers ME, Lister JA, Steingrimsson E, Voet T, Ponting CP, Patton EE. 2019. Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease. Cancer Res 79: 5769-5784. PubMed Fulltext
  16. Kerr SM, Klaric L, Halachev M, Hayward C, Boutin TS, Meynert AM, Semple CA, Tuiskula AM, Swan H, Santoyo-Lopez J, Vitart V, Haley C, Dean J, Miedzybrodzka Z, Aitman TJ, Wilson JF. 2019. An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort. Sci Rep 9: 10964. PubMed Fulltext
  17. Hollis RL, Carmichael J, Meynert AM, Churchman M, Hallas-Potts A, Rye T, MacKean M, Nussey F, Semple CA, Herrington CS, Gourley C. 2019. Clinical and molecular characterization of ovarian carcinoma displaying isolated lymph node relapse. Am J Obstet Gynecol 221: 245.e1-245.e15. PubMed Fulltext
  18. Scottish Science Advisory Council and expert panel writing group. 2019. Informing the Future of Genomic Medicine in Scotland. Fulltext
  19. Ballinger TJ, Bouwman BAM, Mirzazadeh R, Garnerone S, Crosetto N, Semple CA. 2019. Modeling double strand break susceptibility to interrogate structural variation in cancer. Genome Biol 20: 28. PubMed Fulltext
  20. Ewing A, Semple CA. 2018. Breaking point: the genesis and impact of structural variation in tumours. F1000Res 7(F1000 Faculty Rev): 1814. PubMed Fulltext
  21. Logan CV, Murray JE, Parry DA, Robertson A, Bellelli R, Tarnauskaitė Ž, Challis R, Cleal L, Borel V, Fluteau A, Santoyo-Lopez J; SGP Consortium, Aitman T, Barroso I, Basel D, Bicknell LS, Goel H, Hu H, Huff C, Hutchison M, Joyce C, Knox R, Lacroix AE, Langlois S, McCandless S, McCarrier J, Metcalfe KA, Morrissey R, Murphy N, Netchine I, O’Connell SM, Olney AH, Paria N, Rosenfeld JA, Sherlock M, Syverson E, White PC, Wise C, Yu Y, Zacharin M, Banerjee I, Reijns M, Bober MB, Semple RK, Boulton SJ, Rios JJ, Jackson AP. 2018. DNA Polymerase Epsilon Deficiency Causes IMAGe Syndrome with Variable Immunodeficiency. Am J Hum Genet 103: 1038.  PubMed Fulltext
  22. Malavasi ELV, Economides KD, Grünewald E, Makedonopoulou P, Gautier P, Mackie S, Murphy LC, Murdoch H, Crummie D, Ogawa F, McCartney DL, O’Sullivan ST, Burr K, Torrance HS, Phillips J, Bonneau M, Anderson SM, Perry P, Pearson M, Constantinides C, Davidson-Smith H, Kabiri M, Duff B, Johnstone M, Polites HG, Lawrie SM, Blackwood DH, Semple CA, Evans KL, Didier M, Chandran S, McIntosh AM, Price DJ, Houslay MD, Porteous DJ, Millar JK. 2018. DISC1 regulates N-methyl-D-aspartate receptor dynamics: abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness. Transl Psychiatry 8: 184. PubMed Fulltext
  23. Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, FANTOM Consortium, Aitken S, Semple CA. 2018. Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. Open Biol: 8(8). pii: 180011. PubMed Fulltext
  24. Kaiser VB, Semple CA. 2018. Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline. Genome Biol 19: 101. PubMed Fulltext
  25. Hollis RL, Meynert AM, Churchman M, Rye T, Mackean M, Nussey F, Arends MJ, Sims AH, Semple CA, Herrington CS, Gourley C. 2018. Enhanced response rate to pegylated liposomal doxorubicin in high grade serous ovarian carcinomas harbouring BRCA1 and BRCA2 aberrations. BMC Cancer 18: 16. PubMed Fulltext
  26. Aitken S, Semple CA. 2017. The circadian dynamics of small nucleolar RNA in the mouse liver. J R Soc Interface: 14(130). PubMed Fulltext
  27. Kaiser VB, Semple CA. 2017. When TADs go bad: chromatin structure and nuclear organisation in human disease. F1000Res 6(F1000 Faculty Rev): 314. PubMed Fulltext
  28. 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. Fulltext
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. Prendergast JG, Chambers EV, Semple CA. 2014. Sequence level mechanisms of human epigenome evolution. Genome Biol Evol 6: 1758-71. PubMed Fulltext
  35. 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
  36. FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014. A promoter-level mammalian expression atlas. Nature 507: 462-70. PubMed Fulltext
  37. Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR. 2013. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol 14: R146. PubMed Fulltext
  38. 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
  39. Prendergast JG, Semple CA. 2013. Side effects: substantial non-neutral evolution flanking regulatory sites. PLoS Genet 9: e1003528. PubMed Fulltext
  40. 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
  41. Chambers EV, Semple CA. 2013. Chromatin structure and human genome evolution. In ‘Encyclopedia of Life Sciences’. John Wiley & Sons Ltd, London.
  42. Kindt AS, Navarro P, Semple CA, Haley CS. 2013. The genomic signature of trait-associated variants. BMC Genomics 14: 108. PubMed Fulltext
  43. Dunlop MG et al. 2012. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nature Genet 44: 770-776. PubMed Fulltext
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. Chambers EV, Kindt AS, Semple CA. 2011. Opening sequence: computational genomics in the era of high-throughput sequencing. Genome Biol 12: 310. PubMed Fulltext
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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).
  55. 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
  56. 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
  57. 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
  58. Semple CA, Taylor MS. 2009. Molecular biology: The structure of change. Science 323: 347-348. PubMed
  59. Michlewski G, Guil S, Semple CA, Caceres JF. 2008. Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol Cell 32: 383-393. PubMed
  60. Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. 2008. Rapidly evolving human promoter regions. Nat Genet 40: 1262-1263. PubMed
  61. 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
  62. 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
  63. Semple CA. 2008. Chromatin structure and human genome evolution. In ‘Encyclopedia of Life Sciences’. John Wiley & Sons Ltd, London.
  64. 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
  65. 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.
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA. 2006. Heterotachy in mammalian promoter evolution. PLOS Genet 2(4): e30. PubMed
  74. 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
  75. 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
  76. The FANTOM Consortium. 2005. The Transcriptional Landscape of the Mammalian Genome. Science 309: 1559-1563. PubMed
  77. 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
  78. 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
  79. 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
  80. 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
  81. Turner FS, Clutterbuck DR, Semple CAM. 2003. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol 4: R75. PubMed
  82. 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
  83. Semple CAM. 2003. The comparative proteomics of ubiquitination in mouse. Genome Res 13: 1389-1394. PubMed
  84. Semple CAM, Rolfe M, Dorin JR. 2003. Duplication and selection in the evolution of primate beta-defensin genes. Genome Biol 4(5): R31. PubMed
  85. 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
  86. 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
  87. 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.
  88. 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
  89. 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
  90. 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
  91. 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
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  102. 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
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