Publications

mug_helix


Publications from the past five years.


  • 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 epub 24 June 2020. 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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