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Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions.

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.

PLoS Genet. 2019 Nov 25;15(11):e1008480. doi: 10.1371/journal.pgen.1008480. eCollection 2019 Nov.


Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease.

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.

Cancer Res. 2019 Nov 15;79(22):5769-5784. doi: 10.1158/0008-5472.CAN-19-0037. Epub 2019 Oct 3.


An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort.

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.

Sci Rep. 2019 Jul 29;9(1):10964. doi: 10.1038/s41598-019-47436-6.


Clinical and molecular characterization of ovarian carcinoma displaying isolated lymph node relapse.

Hollis RL, Carmichael J, Meynert AM, Churchman M, Hallas-Potts A, Rye T, MacKean M, Nussey F, Semple CA, Herrington CS, Gourley C.

Am J Obstet Gynecol. 2019 Sep;221(3):245.e1-245.e15. doi: 10.1016/j.ajog.2019.04.035. Epub 2019 May 2.


Modeling double strand break susceptibility to interrogate structural variation in cancer.

Ballinger TJ, Bouwman BAM, Mirzazadeh R, Garnerone S, Crosetto N, Semple CA.

Genome Biol. 2019 Feb 8;20(1):28. doi: 10.1186/s13059-019-1635-1.


DISC1 regulates N-methyl-D-aspartate receptor dynamics: abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness.

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.

Transl Psychiatry. 2018 Sep 6;8(1):184. doi: 10.1038/s41398-018-0228-1.


Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli.

Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y; FANTOM Consortium, Aitken S, Semple CA.

Open Biol. 2018 Aug;8(8). pii: 180011. doi: 10.1098/rsob.180011.


Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline.

Kaiser VB, Semple CA.

Genome Biol. 2018 Jul 30;19(1):101. doi: 10.1186/s13059-018-1483-4.


Enhanced response rate to pegylated liposomal doxorubicin in high grade serous ovarian carcinomas harbouring BRCA1 and BRCA2 aberrations.

Hollis RL, Meynert AM, Churchman M, Rye T, Mackean M, Nussey F, Arends MJ, Sims AH, Semple CA, Herrington CS, Gourley C.

BMC Cancer. 2018 Jan 3;18(1):16. doi: 10.1186/s12885-017-3981-2.


The circadian dynamics of small nucleolar RNA in the mouse liver.

Aitken S, Semple CA.

J R Soc Interface. 2017 May;14(130). pii: 20170034. doi: 10.1098/rsif.2017.0034.


When TADs go bad: chromatin structure and nuclear organisation in human disease.

Kaiser VB, Semple CA.

F1000Res. 2017 Mar 24;6. pii: F1000 Faculty Rev-314. doi: 10.12688/f1000research.10792.1. eCollection 2017. Review.


Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types.

Kaiser VB, Taylor MS, Semple CA.

PLoS Genet. 2016 Aug 4;12(8):e1006207. doi: 10.1371/journal.pgen.1006207. eCollection 2016 Aug.


Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

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.

Mol Syst Biol. 2015 Dec 23;11(12):852. doi: 10.15252/msb.20156492.


Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

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.

Hum Mol Genet. 2015 Oct 1;24(19):5464-74. doi: 10.1093/hmg/ddv272. Epub 2015 Jul 14.


Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization.

Moore BL, Aitken S, Semple CA.

Genome Biol. 2015 May 27;16:110. doi: 10.1186/s13059-015-0661-x.


Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

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.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004217. doi: 10.1371/journal.pcbi.1004217. eCollection 2015 Apr. Erratum in: PLoS Comput Biol. 2017 Feb 10;13(2):e1005279.


Sequence-level mechanisms of human epigenome evolution.

Prendergast JG, Chambers EV, Semple CA.

Genome Biol Evol. 2014 Jun 24;6(7):1758-71. doi: 10.1093/gbe/evu142.


Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid.

Wei WH, Guo Y, Kindt AS, Merriman TR, Semple CA, Wang K, Haley CS.

Hum Mol Genet. 2014 Oct 1;23(19):5061-8. doi: 10.1093/hmg/ddu227. Epub 2014 May 12.


Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.

Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR.

Genome Biol. 2013 Dec 24;14(12):R146. doi: 10.1186/gb-2013-14-12-r146.


Properties of local interactions and their potential value in complementing genome-wide association studies.

Wei W, Gyenesei A, Semple CA, Haley CS.

PLoS One. 2013 Aug 5;8(8):e71203. doi: 10.1371/journal.pone.0071203. Print 2013.


Side effects: substantial non-neutral evolution flanking regulatory sites.

Prendergast JG, Semple CA.

PLoS Genet. 2013 May;9(5):e1003528. doi: 10.1371/journal.pgen.1003528. Epub 2013 May 30. No abstract available.


Divergence of mammalian higher order chromatin structure is associated with developmental loci.

Chambers EV, Bickmore WA, Semple CA.

PLoS Comput Biol. 2013 Apr;9(4):e1003017. doi: 10.1371/journal.pcbi.1003017. Epub 2013 Apr 4.


The genomic signature of trait-associated variants.

Kindt AS, Navarro P, Semple CA, Haley CS.

BMC Genomics. 2013 Feb 18;14:108. doi: 10.1186/1471-2164-14-108.


BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.

Gyenesei A, Moody J, Laiho A, Semple CA, Haley CS, Wei WH.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W628-32. doi: 10.1093/nar/gks550. Epub 2012 Jun 11.


High-throughput analysis of epistasis in genome-wide association studies with BiForce.

Gyenesei A, Moody J, Semple CA, Haley CS, Wei WH.

Bioinformatics. 2012 Aug 1;28(15):1957-64. doi: 10.1093/bioinformatics/bts304. Epub 2012 May 21. Erratum in: Bioinformatics. 2013 Oct 15;29(20):2667-8.


A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci.

Prendergast JG, Tong P, Hay DC, Farrington SM, Semple CA.

Epigenetics Chromatin. 2012 May 19;5(1):6. doi: 10.1186/1756-8935-5-6.


Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, 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.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. doi: 10.1073/pnas.1110156109. Epub 2012 Mar 26.


Opening sequence: computational genomics in the era of high-throughput sequencing.

Chambers EV, Kindt AS, Semple CA.

Genome Biol. 2011 Dec 28;12(12):310. doi: 10.1186/gb-2011-12-12-310.


Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway.

Nimmo ER, Prendergast JG, Aldhous MC, Kennedy NA, Henderson P, Drummond HE, Ramsahoye BH, Wilson DC, Semple CA, Satsangi J.

Inflamm Bowel Dis. 2012 May;18(5):889-99. doi: 10.1002/ibd.21912. Epub 2011 Oct 21.


Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.

Prendergast JG, Semple CA.

Genome Res. 2011 Nov;21(11):1777-87. doi: 10.1101/gr.122275.111. Epub 2011 Sep 8.


Human β-defensin 3 affects the activity of pro-inflammatory pathways associated with MyD88 and TRIF.

Semple F, MacPherson H, Webb S, Cox SL, Mallin LJ, Tyrrell C, Grimes GR, Semple CA, Nix MA, Millhauser GL, Dorin JR.

Eur J Immunol. 2011 Nov;41(11):3291-300. doi: 10.1002/eji.201141648. Epub 2011 Sep 6.


A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

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.

PLoS Biol. 2011 Jan 18;9(1):e1000582. doi: 10.1371/journal.pbio.1000582.


The retroviral proteinase active site and the N-terminus of Ddi1 are required for repression of protein secretion.

White RE, Dickinson JR, Semple CA, Powell DJ, Berry C.

FEBS Lett. 2011 Jan 3;585(1):139-42. doi: 10.1016/j.febslet.2010.11.026. Epub 2010 Nov 19.


New ATPase regulators--p97 goes to the PUB.

Madsen L, Seeger M, Semple CA, Hartmann-Petersen R.

Int J Biochem Cell Biol. 2009 Dec;41(12):2380-8. doi: 10.1016/j.biocel.2009.05.017. Epub 2009 Jun 2. Review.


The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.


Thioredoxin Txnl1/TRP32 is a redox-active cofactor of the 26 S proteasome.

Andersen KM, Madsen L, Prag S, Johnsen AH, Semple CA, Hendil KB, Hartmann-Petersen R.

J Biol Chem. 2009 May 29;284(22):15246-54. doi: 10.1074/jbc.M900016200. Epub 2009 Apr 6.


Molecular biology. The structure of change.

Semple CA, Taylor MS.

Science. 2009 Jan 16;323(5912):347-8. doi: 10.1126/science.1169408. No abstract available.


Posttranscriptional regulation of miRNAs harboring conserved terminal loops.

Michlewski G, Guil S, Semple CA, Cáceres JF.

Mol Cell. 2008 Nov 7;32(3):383-93. doi: 10.1016/j.molcel.2008.10.013.


Rapidly evolving human promoter regions.

Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA.

Nat Genet. 2008 Nov;40(11):1262-3; author reply 1263-4. doi: 10.1038/ng1108-1262. No abstract available.


Ubxd1 is a novel co-factor of the human p97 ATPase.

Madsen L, Andersen KM, Prag S, Moos T, Semple CA, Seeger M, Hartmann-Petersen R.

Int J Biochem Cell Biol. 2008;40(12):2927-42. doi: 10.1016/j.biocel.2008.06.008. Epub 2008 Jul 5.


Chromatin structure and evolution in the human genome.

Prendergast JG, Campbell H, Gilbert N, Dunlop MG, Bickmore WA, Semple CA.

BMC Evol Biol. 2007 May 9;7:72.


Characterisation of the nascent polypeptide-associated complex in fission yeast.

Andersen KM, Semple CA, Hartmann-Petersen R.

Mol Biol Rep. 2007 Dec;34(4):275-81. Epub 2007 Jan 9.


Disruption of Ledgf/Psip1 results in perinatal mortality and homeotic skeletal transformations.

Sutherland HG, Newton K, Brownstein DG, Holmes MC, Kress C, Semple CA, Bickmore WA.

Mol Cell Biol. 2006 Oct;26(19):7201-10.


The changing of the guard: Molecular diversity and rapid evolution of beta-defensins.

Semple CA, Gautier P, Taylor K, Dorin JR.

Mol Divers. 2006 Nov;10(4):575-84. Review.


Mouse MAELSTROM: the link between meiotic silencing of unsynapsed chromatin and microRNA pathway?

Costa Y, Speed RM, Gautier P, Semple CA, Maratou K, Turner JM, Cooke HJ.

Hum Mol Genet. 2006 Aug 1;15(15):2324-34. Epub 2006 Jun 20.


Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W.

Nucleic Acids Res. 2006 Jun 6;34(10):3067-81. Print 2006.


Heterotachy in mammalian promoter evolution.

Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA.

PLoS Genet. 2006 Apr;2(4):e30. Epub 2006 Apr 28.


Genome-wide analysis of mammalian promoter architecture and evolution.

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.

Nat Genet. 2006 Jun;38(6):626-35. Epub 2006 Apr 28. Erratum in: Nat Genet. 2007 Sep;39(9):1174.


Beta-defensin evolution: selection complexity and clues for residues of functional importance.

Semple CA, Taylor K, Eastwood H, Barran PE, Dorin JR.

Biochem Soc Trans. 2006 Apr;34(Pt 2):257-62. Review.


Dazl binds in vivo to specific transcripts and can regulate the pre-meiotic translation of Mvh in germ cells.

Reynolds N, Collier B, Maratou K, Bingham V, Speed RM, Taggart M, Semple CA, Gray NK, Cooke HJ.

Hum Mol Genet. 2005 Dec 15;14(24):3899-909. Epub 2005 Nov 8.


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