Publications

mug_helix

Key Publications

  • 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
  • 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
  • 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
  • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. 2020. Pan-cancer analysis of whole genomes. Nature 578: 82-93. PubMed Fulltext
  • 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
  • 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

Publications from the past five years

  • Diego Chillon Pino, Mihaly Badonyi, Colin A Semple, Joseph A Marsh. 2024. Protein structural context of cancer mutations reveals molecular mechanisms and identifies novel candidate driver genes. bioRxiv 2024.03.21.586131; doi: https://doi.org/10.1101/2024.03.21.586131
  • Vera B. Kaiser, Colin A. Semple. 2024. Stage-resolved chromatin conformation dynamics during human meiosis. bioRxiv 2024.02.29.582729; doi: https://doi.org/10.1101/2024.02.29.582729
  • Ailith Ewing, Alison Meynert, Ryan Silk, Stuart Aitken, Devin P. Bendixsen, Michael Churchman, Stuart L. Brown, Alhafidz Hamdan, Joanne Mattocks, Graeme R. Grimes, Tracy Ballinger, Robert L. Hollis, C. Simon Herrington, John P. Thomson, Kitty Sherwood, Thomas Parry, Edward Esiri-Bloom, Clare Bartos, Ian Croy, Michelle Ferguson, Mairi Lennie, Trevor McGoldrick, Neil McPhail, Nadeem Siddiqui, Rosalind Glasspool, Melanie Mackean, Fiona Nussey, Brian McDade, Darren Ennis, The Scottish Genomes Partnership, Lynn McMahon, Athena Matakidou, Brian Dougherty, Ruth March, J. Carl Barrett, Iain A. McNeish, Andrew V. Biankin, Patricia Roxburgh, Charlie Gourley, Colin A. Semple. 2024. Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer. bioRxiv 2024.01.12.575376; doi: https://doi.org/10.1101/2024.01.12.575376
  • Anagha Krishna, Alison Meynert, Martijn Kelder, Ailith Ewing, Shahida Sheraz, Anna Ferrer-Vaquer, Graeme Grimes, Hannes Becher, Ryan Silk, Colin A Semple, Timothy Kendall, Anna-Katerina Hadjantonakis, Tom Bird, Joseph A Marsh, Peter Hohenstein, Andrew J Wood, Derya D Ozdemir. 2023. Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits. bioRxiv 2023.11.09.566307; doi: https://doi.org/10.1101/2023.11.09.566307
  • Mihail Halachev, Elvina Gountouna, Alison Meynert, Regeneron Genetics Center, Gannie Tzoneva, Alan R. Shuldiner, Colin A. Semple, James F. Wilson. 2022. Regionally enriched rare deleterious exonic variants in the UK and Ireland. bioRxiv 2022.09.19.508526; doi: https://doi.org/10.1101/2022.09.19.508526
  • Craig J. Anderson, Lana Talmane, Juliet Luft, Michael D. Nicholson, John Connelly, Oriol Pich, Susan Campbell, Vasavi Sundaram, Frances Connor, Paul A. Ginno, Liver Cancer Evolution Consortium, Núria López-Bigas, Paul Flicek, Colin A. Semple, Duncan T. Odom, Sarah J. Aitken, Martin S. Taylor. 2022. Strand-resolved mutagenicity of DNA damage and repair. bioRxiv 2022.06.10.495644; doi: https://doi.org/10.1101/2022.06.10.495644
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. 2020. Pan-cancer analysis of whole genomes. Nature 578: 82-93. PubMed Fulltext
  • 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
  • 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
  • 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
  • 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
  • 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
  • Ewing A, Semple CA. 2018. Breaking point: the genesis and impact of structural variation in tumours. F1000Res 7(F1000 Faculty Rev):1814. PubMed Fulltext
  • 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
  • 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
  • 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
  • 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
  • Aitken S, Semple CA. 2017. The circadian dynamics of small nucleolar RNA in the mouse liver. J R Soc Interface: 14(130). PubMed Fulltext
  • 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
  • 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