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Items: 35

1.

Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors.

Cejas P, Drier Y, Dreijerink KMA, Brosens LAA, Deshpande V, Epstein CB, Conemans EB, Morsink FHM, Graham MK, Valk GD, Vriens MR, Castillo CF, Ferrone CR, Adar T, Bowden M, Whitton HJ, Da Silva A, Font-Tello A, Long HW, Gaskell E, Shoresh N, Heaphy CM, Sicinska E, Kulke MH, Chung DC, Bernstein BE, Shivdasani RA.

Nat Med. 2019 Jul 1. doi: 10.1038/s41591-019-0493-4. [Epub ahead of print]

PMID:
31263286
2.

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin CA, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Shoresh N, Epstein CB, de Laat W, Brown JD, Schnabel RB, Bernstein BE, Kathiresan S.

Cell. 2017 Jul 27;170(3):522-533.e15. doi: 10.1016/j.cell.2017.06.049.

3.

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq.

Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C, Goren A.

Epigenetics Chromatin. 2016 Nov 4;9:49. eCollection 2016.

4.

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.

Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE.

Cancer Discov. 2015 Oct;5(10):1058-71. doi: 10.1158/2159-8290.CD-15-0370. Epub 2015 Jul 30.

5.

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.

6.

Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.

Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED.

Nat Cell Biol. 2015 Jan;17(1):44-56. doi: 10.1038/ncb3080. Epub 2014 Dec 15.

7.

Genetic and epigenetic fine mapping of causal autoimmune disease variants.

Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE.

Nature. 2015 Feb 19;518(7539):337-43. doi: 10.1038/nature13835. Epub 2014 Oct 29.

8.

Comparative analysis of metazoan chromatin organization.

Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

9.

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.

De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA.

Nat Neurosci. 2014 Sep;17(9):1156-63. doi: 10.1038/nn.3786. Epub 2014 Aug 17.

10.

Impact of sequencing depth in ChIP-seq experiments.

Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.

Nucleic Acids Res. 2014 May;42(9):e74. doi: 10.1093/nar/gku178. Epub 2014 Mar 5.

11.

Recommendations for the design and analysis of epigenome-wide association studies.

Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA.

Nat Methods. 2013 Oct;10(10):949-55. doi: 10.1038/nmeth.2632. Review.

PMID:
24076989
12.

Genome-wide chromatin state transitions associated with developmental and environmental cues.

Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE.

Cell. 2013 Jan 31;152(3):642-54. doi: 10.1016/j.cell.2012.12.033. Epub 2013 Jan 17.

13.

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H.

Cell. 2012 Jun 22;149(7):1474-87. doi: 10.1016/j.cell.2012.04.035.

14.

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE.

Cell. 2011 Dec 23;147(7):1628-39. doi: 10.1016/j.cell.2011.09.057.

15.

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.

Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A.

PLoS Genet. 2011 Dec;7(12):e1002389. doi: 10.1371/journal.pgen.1002389. Epub 2011 Dec 8.

16.

Mapping and analysis of chromatin state dynamics in nine human cell types.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE.

Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.

17.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF.

Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19.

18.

PTK6 regulates IGF-1-induced anchorage-independent survival.

Irie HY, Shrestha Y, Selfors LM, Frye F, Iida N, Wang Z, Zou L, Yao J, Lu Y, Epstein CB, Natesan S, Richardson AL, Polyak K, Mills GB, Hahn WC, Brugge JS.

PLoS One. 2010 Jul 23;5(7):e11729. doi: 10.1371/journal.pone.0011729.

19.

SIT4 regulation of Mig1p-mediated catabolite repression in Saccharomyces cerevisiae.

Jin C, Barrientos A, Epstein CB, Butow RA, Tzagoloff A.

FEBS Lett. 2007 Dec 11;581(29):5658-63. Epub 2007 Nov 20.

20.

An empirical Bayesian significance test of cDNA library data.

Ge N, Epstein CB.

J Comput Biol. 2004;11(6):1175-88.

PMID:
15662205
21.
22.
23.

Numerical methods for handling uncertainty in microarray data: an example analyzing perturbed mitochondrial function in yeast.

Epstein CB, Hale W 4th, Butow RA.

Methods Cell Biol. 2001;65:439-52. No abstract available.

PMID:
11381609
24.

Identification of partial loss of function p53 gene mutations utilizing a yeast-based functional assay.

Kovvali GK, Mehta B, Epstein CB, Lutzker SG.

Nucleic Acids Res. 2001 Mar 1;29(5):E28.

25.

Genome-wide responses to mitochondrial dysfunction.

Epstein CB, Waddle JA, Hale W 4th, Davé V, Thornton J, Macatee TL, Garner HR, Butow RA.

Mol Biol Cell. 2001 Feb;12(2):297-308.

26.

MAD: a suite of tools for microarray data management and processing.

Liao B, Hale W, Epstein CB, Butow RA, Garner HR.

Bioinformatics. 2000 Oct;16(10):946-7.

PMID:
11120686
27.

Microarray technology - enhanced versatility, persistent challenge.

Epstein CB, Butow RA.

Curr Opin Biotechnol. 2000 Feb;11(1):36-41. Review.

PMID:
10679339
28.
29.

A genetic approach to mapping the p53 binding site in the MDM2 protein.

Freedman DA, Epstein CB, Roth JC, Levine AJ.

Mol Med. 1997 Apr;3(4):248-59.

30.

The spectrum of mutations at the p53 locus. Evidence for tissue-specific mutagenesis, selection of mutant alleles, and a "gain of function" phenotype.

Levine AJ, Wu MC, Chang A, Silver A, Attiyeh EF, Lin J, Epstein CB.

Ann N Y Acad Sci. 1995 Sep 30;768:111-28. Review. No abstract available.

PMID:
8526340
31.
32.

CLB5: a novel B cyclin from budding yeast with a role in S phase.

Epstein CB, Cross FR.

Genes Dev. 1992 Sep;6(9):1695-706.

33.

A method for the estimation of historical sulfate concentrations in natural freshwaters.

Epstein CB.

Environ Sci Technol. 1988 Dec 1;22(12):1460-3. doi: 10.1021/es00177a012. No abstract available.

PMID:
22200474
34.

Response: Acid deposition in the Western United States.

Oppenheimer M, Epstein CB, Yuhnke RE.

Science. 1986 Jul 4;233(4759):12-4. No abstract available.

PMID:
17812878
35.

Acid deposition, smelter emissions, and the linearity issue in the Western United States.

Oppenheimer M, Epstein CB, Yuhnke RE.

Science. 1985 Aug 30;229(4716):859-62.

PMID:
17777926

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