Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 43

1.

Histone Chaperone Paralogs Have Redundant, Co-operative and Divergent Functions in Yeast.

Savic N, Shortill SP, Bilenky M, Dobbs JM, Dilworth D, Hirst M, Nelson CJ.

Genetics. 2019 Oct 11. pii: genetics.302235.2019. doi: 10.1534/genetics.119.302235. [Epub ahead of print]

2.

Hepatocyte Nuclear Factor 4-Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver.

Thakur A, Wong JCH, Wang EY, Lotto J, Kim D, Cheng JC, Mingay M, Cullum R, Moudgil V, Ahmed N, Tsai SH, Wei W, Walsh CP, Stephan T, Bilenky M, Fuglerud BM, Karimi MM, Gonzalez FJ, Hirst M, Hoodless PA.

Hepatology. 2019 Oct;70(4):1360-1376. doi: 10.1002/hep.30631. Epub 2019 May 15.

PMID:
30933372
3.

The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability.

Dilworth D, Gudavicius G, Xu X, Boyce AKJ, O'Sullivan C, Serpa JJ, Bilenky M, Petrochenko EV, Borchers CH, Hirst M, Swayne LA, Howard P, Nelson CJ.

Nucleic Acids Res. 2018 Mar 16;46(5):2459-2478. doi: 10.1093/nar/gky008.

4.

Characterization of the human thyroid epigenome.

Siu C, Wiseman S, Gakkhar S, Heravi-Moussavi A, Bilenky M, Carles A, Sierocinski T, Tam A, Zhao E, Kasaian K, Moore RA, Mungall AJ, Walker B, Thomson T, Marra MA, Hirst M, Jones SJM.

J Endocrinol. 2017 Nov;235(2):153-165. doi: 10.1530/JOE-17-0145. Epub 2017 Aug 14.

PMID:
28808080
5.

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b.

Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M.

Epigenetics Chromatin. 2017 Jul 12;10:36. doi: 10.1186/s13072-017-0143-3. eCollection 2017.

6.

Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia.

Mingay M, Chaturvedi A, Bilenky M, Cao Q, Jackson L, Hui T, Moksa M, Heravi-Moussavi A, Humphries RK, Heuser M, Hirst M.

Leukemia. 2018 Jan;32(1):11-20. doi: 10.1038/leu.2017.171. Epub 2017 Jun 2.

7.

Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility.

Lorzadeh A, Bilenky M, Hammond C, Knapp DJHF, Li L, Miller PH, Carles A, Heravi-Moussavi A, Gakkhar S, Moksa M, Eaves CJ, Hirst M.

Cell Rep. 2016 Nov 15;17(8):2112-2124. doi: 10.1016/j.celrep.2016.10.055.

8.

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJHF, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJM, Aparicio S, Hirst M, Eaves CJ.

Cell Rep. 2016 Nov 15;17(8):2060-2074. doi: 10.1016/j.celrep.2016.10.058.

9.

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.

Chun HE, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Palmquist DL, He A, Long W, Goya R, Ng M, LeBlanc VG, Pleasance E, Thiessen N, Wong T, Chuah E, Zhao YJ, Schein JE, Gerhard DS, Taylor MD, Mungall AJ, Moore RA, Ma Y, Jones SJM, Perlman EJ, Hirst M, Marra MA.

Cancer Cell. 2016 Mar 14;29(3):394-406. doi: 10.1016/j.ccell.2016.02.009.

10.

Divergent clonal selection dominates medulloblastoma at recurrence.

Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD.

Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13.

11.

Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells.

Nguyen LV, Pellacani D, Lefort S, Kannan N, Osako T, Makarem M, Cox CL, Kennedy W, Beer P, Carles A, Moksa M, Bilenky M, Balani S, Babovic S, Sun I, Rosin M, Aparicio S, Hirst M, Eaves CJ.

Nature. 2015 Dec 10;528(7581):267-71. doi: 10.1038/nature15742. Epub 2015 Dec 2.

PMID:
26633636
12.

SOX9 modulates the expression of key transcription factors required for heart valve development.

Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, Zhao Y, Jones SJ, Marra MA, Underhill TM, Hoodless PA.

Development. 2015 Dec 15;142(24):4340-50. doi: 10.1242/dev.125252. Epub 2015 Nov 2.

13.

Precursor States of Brain Tumor Initiating Cell Lines Are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes.

Cusulin C, Chesnelong C, Bose P, Bilenky M, Kopciuk K, Chan JA, Cairncross JG, Jones SJ, Marra MA, Luchman HA, Weiss S.

Stem Cell Reports. 2015 Jul 14;5(1):1-9. doi: 10.1016/j.stemcr.2015.05.010. Epub 2015 Jun 18.

14.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

15.

Intermediate DNA methylation is a conserved signature of genome regulation.

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF.

Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.

16.

Epigenetic and transcriptional determinants of the human breast.

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M.

Nat Commun. 2015 Feb 18;6:6351. doi: 10.1038/ncomms7351.

17.

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB.

Nat Commun. 2014 Nov 25;5:5442. doi: 10.1038/ncomms6442.

18.

Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation.

Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Garside VC, Bilenky M, Griffith M, Morrissy AS, Robertson GA, Thiessen N, Zhao Y, Chen Q, Pan D, Jones SJM, Marra MA, Hoodless PA.

Cell Rep. 2014 Oct 9;9(1):261-271. doi: 10.1016/j.celrep.2014.08.046. Epub 2014 Sep 25.

19.

A transgenic mouse model demonstrating the oncogenic role of mutations in the polycomb-group gene EZH2 in lymphomagenesis.

Berg T, Thoene S, Yap D, Wee T, Schoeler N, Rosten P, Lim E, Bilenky M, Mungall AJ, Oellerich T, Lee S, Lai CK, Umlandt P, Salmi A, Chang H, Yue L, Lai D, Cheng SW, Morin RD, Hirst M, Serve H, Marra MA, Morin GB, Gascoyne RD, Aparicio SA, Humphries RK.

Blood. 2014 Jun 19;123(25):3914-24. doi: 10.1182/blood-2012-12-473439. Epub 2014 May 6.

PMID:
24802772
20.

Delineating MEIS1 cis-regulatory elements active in hematopoietic cells.

Xiang P, Wei W, Lo C, Rosten P, Hou J, Hoodless PA, Bilenky M, Bonifer C, Cockerill PN, Kirkpatrick A, Gottgens B, Hirst M, Humphries KR.

Leukemia. 2014 Feb;28(2):433-6. doi: 10.1038/leu.2013.287. Epub 2013 Oct 7. No abstract available.

PMID:
24097337
21.

MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes.

Qin ZS, Bilenky M, Su G, Jones SJ.

Front Biosci (Elite Ed). 2013 Jan 1;5:785-97.

PMID:
23277033
22.

Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse.

Vrljicak P, Cullum R, Xu E, Chang AC, Wederell ED, Bilenky M, Jones SJ, Marra MA, Karsan A, Hoodless PA.

PLoS One. 2012;7(7):e40815. doi: 10.1371/journal.pone.0040815. Epub 2012 Jul 16.

23.

Identification and characterization of Hoxa9 binding sites in hematopoietic cells.

Huang Y, Sitwala K, Bronstein J, Sanders D, Dandekar M, Collins C, Robertson G, MacDonald J, Cezard T, Bilenky M, Thiessen N, Zhao Y, Zeng T, Hirst M, Hero A, Jones S, Hess JL.

Blood. 2012 Jan 12;119(2):388-98. doi: 10.1182/blood-2011-03-341081. Epub 2011 Nov 9.

24.

Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms.

Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC, Mager DL.

PLoS Genet. 2011 Sep;7(9):e1002301. doi: 10.1371/journal.pgen.1002301. Epub 2011 Sep 29.

25.

H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing.

Maksakova IA, Goyal P, Bullwinkel J, Brown JP, Bilenky M, Mager DL, Singh PB, Lorincz MC.

Epigenetics Chromatin. 2011 Jul 20;4(1):12. doi: 10.1186/1756-8935-4-12.

26.

Cell of origin in AML: susceptibility to MN1-induced transformation is regulated by the MEIS1/AbdB-like HOX protein complex.

Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK.

Cancer Cell. 2011 Jul 12;20(1):39-52. doi: 10.1016/j.ccr.2011.06.020.

27.

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs.

Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC.

Cell Stem Cell. 2011 Jun 3;8(6):676-87. doi: 10.1016/j.stem.2011.04.004.

28.

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.

Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA.

Genome Biol. 2010;11(8):R82. doi: 10.1186/gb-2010-11-8-r82. Epub 2010 Aug 9.

29.

Conserved role of intragenic DNA methylation in regulating alternative promoters.

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF.

Nature. 2010 Jul 8;466(7303):253-7. doi: 10.1038/nature09165.

30.

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.

Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJ, Hoodless PA.

Genome Res. 2010 Aug;20(8):1037-51. doi: 10.1101/gr.104356.109. Epub 2010 Jun 15.

31.

Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern.

Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ.

BMC Genomics. 2010 Feb 23;11:131. doi: 10.1186/1471-2164-11-131.

32.

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements.

Sleumer MC, Bilenky M, He A, Robertson G, Thiessen N, Jones SJ.

Nucleic Acids Res. 2009 Mar;37(4):1323-34. doi: 10.1093/nar/gkn1041. Epub 2009 Jan 16.

33.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

34.

Identification of a set of genes showing regionally enriched expression in the mouse brain.

D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ.

BMC Neurosci. 2008 Jul 14;9:66. doi: 10.1186/1471-2202-9-66.

35.

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.

Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA.

Nucleic Acids Res. 2008 Aug;36(14):4549-64. doi: 10.1093/nar/gkn382. Epub 2008 Jul 8.

36.

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.

Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ.

Bioinformatics. 2008 Aug 1;24(15):1729-30. doi: 10.1093/bioinformatics/btn305. Epub 2008 Jul 3.

37.

ORegAnno: an open-access community-driven resource for regulatory annotation.

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.

38.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7. Epub 2007 Jun 11.

PMID:
17558387
39.

The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine.

McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJ, Moerman DG, Robertson AG.

Dev Biol. 2007 Feb 15;302(2):627-45. Epub 2006 Oct 21.

40.

THOR: targeted high-throughput ortholog reconstructor.

Bainbridge MN, Warren RL, He A, Bilenky M, Robertson AG, Jones SJ.

Bioinformatics. 2007 Oct 1;23(19):2622-4. Epub 2006 Oct 11.

PMID:
17038343
41.

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.

Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ.

Bioinformatics. 2006 Mar 1;22(5):637-40. Epub 2006 Jan 5.

PMID:
16397004
42.

cisRED: a database system for genome-scale computational discovery of regulatory elements.

Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73.

43.

Sockeye: a 3D environment for comparative genomics.

Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ.

Genome Res. 2004 May;14(5):956-62.

Supplemental Content

Loading ...
Support Center