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Items: 1 to 20 of 35

1.

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

Chun HJ, 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 SJ, Perlman EJ, Hirst M, Marra MA.

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

PMID:
26977886
2.

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.

PMID:
26760213
3.

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
4.

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.

PMID:
26525672
5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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 SJ, Marra MA, Hoodless PA.

Cell Rep. 2014 Oct 9;9(1):261-71. doi: 10.1016/j.celrep.2014.08.046. Epub 2014 Sep 25.

11.

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.

12.

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
13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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