Publications

mug_helix

Key Publications

  • Ewing A, Meynert A, Silk R, Aitken S, Bendixsen DP, Churchman M, Brown SL, Hamdan A, Mattocks J, Grimes GR, Ballinger T, Hollis RL, Simon Herrington C, Thomson JP, Sherwood K, Parry T, Esiri-Bloom E, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D; Scottish Genomes Partnership; McMahon L, Matakidou A, Dougherty B, March R, Carl Barrett J, McNeish IA, Biankin AV, Roxburgh P, Gourley C, Semple CA. 2025. Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer. Nat Commun 16: 5586. 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
  • 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

  • Devin P Bendixen, Fiona Semple, Alastair Ironside, Mustafa İsmail Özkaraca, Natalie Wilson, Alison Meynert, Ailith Ewing, Colin A Semple, Olga OIkonomidou. Frequent Whole-Genome Duplication Events Drive the Genomic Evolution of Triple-Negative Breast Cancer During Neoadjuvant Chemotherapy. bioRxiv 2025.11.17.688693; doi: https://doi.org/10.1101/2025.11.17.688693
  • Maëlle Daunesse, Vasavi Sundaram, Elissavet Kentepozidou, John Connelly, Craig J Anderson, Liver Cancer Evolution Consortium, Núria López-Bigas, Colin Semple, Duncan T Odom, Martin S Taylor, Maša Roller, Sarah J Aitken, Paul Flicek. 2025. Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis. bioRxiv 2025.02.11.637769; doi: https://doi.org/10.1101/2025.02.11.637769
  • Mitchell T Foster, Ailith Ewing, Margaret Frame, Paul M Brennan, Ava Khamseh, Sjoerd V Beentjes, Neil O Carragher, Colin A Semple. 2025. Systematic identification of context-dependent gene-essentiality in Glioblastoma: The GBM-CoDE platform. bioRxiv 2025.01.27.634260; doi: https://doi.org/10.1101/2025.01.27.634260
  • Sarah J Aitken, Frances Connor, Christine Feig, Tim F Rayner, Margus Lukk, Juliet Luft, Stuart Aitken, Claudia Arnedo-Pac, James F Hayes, Michael D Nicholson, Vasavi Sundaram, Jan C Verburg, John Connelly, Craig J Anderson, Mikaela Behm, Susan Campbell, Maelle Daunesse, Ailith Ewing, Vera B Kaiser, Elissavet Kentepozidou, Oriol Pich, Aisling M Redmond, Javier Santoyo-Lopez, Ines Sentis, Lana Talmane, Liver Cancer Evolution Consortium, Paul Flicek, Nuria Lopez-Bigas, Colin A Semple, Martin S Taylor, Duncan T Odom. 2025. Genetic background sets the trajectory of cancer evolution. bioRxiv 2025.01.13.632787; doi: https://doi.org/10.1101/2025.01.13.632787
  • 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
  • Low SSP, Greaves L, Silk R, Semple CA, Gourley C. 2025. Spectrum and Impact of Mitochondrial DNA Mutations in Ovarian Cancer. Int J Mol Sci 26: 11180. PubMed Fulltext
  • Ewing A, Meynert A, Silk R, Aitken S, Bendixsen DP, Churchman M, Brown SL, Hamdan A, Mattocks J, Grimes GR, Ballinger T, Hollis RL, Simon Herrington C, Thomson JP, Sherwood K, Parry T, Esiri-Bloom E, Bartos C, Croy I, Ferguson M, Lennie M, McGoldrick T, McPhail N, Siddiqui N, Glasspool R, Mackean M, Nussey F, McDade B, Ennis D; Scottish Genomes Partnership; McMahon L, Matakidou A, Dougherty B, March R, Carl Barrett J, McNeish IA, Biankin AV, Roxburgh P, Gourley C, Semple CA. 2025. Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer. Nat Commun 16: 5586. PubMed Fulltext
  • Kaiser VB, Semple CA. 2025. CTCF-anchored chromatin loop dynamics during human meiosis. BMC Biol 23: 83. PubMed Fulltext
  • Hollis RL, Churchman M, Grimes GR, Meynert AM, Gautier P, McMahon L, Sherwood K, Oswald AJ, Croy I, Ferguson M, Martin CW, McGoldrick T, McPhail N, Creedon H, Barrett JC, March R, Dougherty BA, Roxburgh P, Ewing A, Herrington CS, Semple CA, Gourley C. 2025. Somatic BRCA1/2 mutations are associated with a similar survival advantage to their germline counterparts in tubo-ovarian high grade serous carcinoma. Eur J Cancer 219:115299. PubMed Fulltext
  • Chillón-Pino D, Badonyi M, Semple CA, Marsh JA. 2024. Protein structural context of cancer mutations reveals molecular mechanisms and candidate driver genes. Cell Rep 43: 114905. PubMed Fulltext
  • Halachev M, Gountouna VE, Meynert A, Tzoneva G, Shuldiner AR, Semple CA, Wilson JF. 2024. Regionally enriched rare deleterious exonic variants in the UK and Ireland. Nat Commun 15: 8454. PubMed Fulltext
  • Anderson CJ, Talmane L, Luft J, Connelly J, Nicholson MD, Verburg JC, Pich O, Campbell S, Giaisi M, Wei PC, Sundaram V, Connor F, Ginno PA, Sasaki T, Gilbert DM; Liver Cancer Evolution Consortium; López-Bigas N, Semple CA, Odom DT, Aitken SJ, Taylor MS. 2024. Strand-resolved mutagenicity of DNA damage and repair. Nature 630: 744-751. PubMed Fulltext
  • 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. PubMed 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