Publications

mug_helix


Publications from the past five years.


  • Aitken S, Semple CA. 2017. The circadian dynamics of small nucleolar RNA in the mouse liver. J R Soc Interface, in press.
  • 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, in press.
  • 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
  • Prendergast JG, Chambers EV, Semple CA. 2014. Sequence level mechanisms of human epigenome evolution. Genome Biol Evol 6: 1758-71. PubMed Fulltext
  • 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
  • FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014. A promoter-level mammalian expression atlas. Nature 507: 462-70. PubMed Fulltext
  • 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
  • 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
  • Prendergast JG, Semple CA. 2013. Side effects: substantial non-neutral evolution flanking regulatory sites. PLoS Genet 9: e1003528. PubMed Fulltext
  • 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
  • Chambers EV, Semple CA. 2013. Chromatin structure and human genome evolution. In ‘Encyclopedia of Life Sciences’. John Wiley & Sons Ltd, London.
  • Kindt AS, Navarro P, Semple CA, Haley CS. 2013. The genomic signature of trait-associated variants. BMC Genomics 14: 108. PubMed Fulltext
  • Dunlop MG et al. 2012. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nature Genet 44: 770-776. PubMed Fulltext
  • 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
  • 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
  • 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
  • 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
  • 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