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1.

Emerging patterns of epigenomic variation.

Milosavljevic A.

Trends Genet. 2011 Jun;27(6):242-50. doi: 10.1016/j.tig.2011.03.001. Epub 2011 Apr 18. Review.

2.

The epigenome and plant development.

He G, Elling AA, Deng XW.

Annu Rev Plant Biol. 2011;62:411-35. doi: 10.1146/annurev-arplant-042110-103806. Review.

PMID:
21438682
3.

Phenotypic diversity and epigenomic variation - The utility of mass spectrometric analysis of DNA methylation.

McLean C, Gluckman P, Sheppard A.

J Proteomics. 2012 Jun 27;75(12):3400-9. doi: 10.1016/j.jprot.2012.01.036. Epub 2012 Feb 14.

PMID:
22353436
4.

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.

PMID:
25693563
5.

Epigenome mapping in normal and disease States.

Maunakea AK, Chepelev I, Zhao K.

Circ Res. 2010 Aug 6;107(3):327-39. doi: 10.1161/CIRCRESAHA.110.222463. Review.

6.

The potential role of epigenomic dysregulation in complex human disease.

Hatchwell E, Greally JM.

Trends Genet. 2007 Nov;23(11):588-95. Epub 2007 Oct 22. Review.

PMID:
17953999
7.

Genome, epigenome and transcriptome analyses of a pair of monozygotic twins discordant for systemic lupus erythematosus.

Furukawa H, Oka S, Matsui T, Hashimoto A, Arinuma Y, Komiya A, Fukui N, Tsuchiya N, Tohma S.

Hum Immunol. 2013 Feb;74(2):170-5. doi: 10.1016/j.humimm.2012.11.007. Epub 2012 Nov 29.

PMID:
23200755
8.

Epigenomic modification and epigenetic regulation in rice.

Zhao Y, Zhou DX.

J Genet Genomics. 2012 Jul 20;39(7):307-15. doi: 10.1016/j.jgg.2012.02.009. Epub 2012 Apr 2. Review.

PMID:
22835977
9.

Mapping human epigenomes.

Rivera CM, Ren B.

Cell. 2013 Sep 26;155(1):39-55. doi: 10.1016/j.cell.2013.09.011. Review.

10.

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools.

Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A.

BMC Bioinformatics. 2014;15 Suppl 7:S2. doi: 10.1186/1471-2105-15-S7-S2. Epub 2014 May 28.

11.

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV.

Am J Hum Genet. 2012 Sep 7;91(3):455-65. doi: 10.1016/j.ajhg.2012.07.024. Epub 2012 Aug 23.

12.

Epigenomic plasticity within populations: its evolutionary significance and potential.

Johnson LJ, Tricker PJ.

Heredity (Edinb). 2010 Jul;105(1):113-21. doi: 10.1038/hdy.2010.25. Epub 2010 Mar 24. Review.

13.

Epigenome sequencing comes of age in development, differentiation and disease mechanism research.

Zhao Q, Zhang Y.

Epigenomics. 2011 Apr;3(2):207-20. doi: 10.2217/epi.10.78. Review.

PMID:
22122282
14.

The decade of the epigenomes?

Martens JH, Stunnenberg HG, Logie C.

Genes Cancer. 2011 Jun;2(6):680-7. doi: 10.1177/1947601911417860.

15.

Putting epigenome comparison into practice.

Milosavljevic A.

Nat Biotechnol. 2010 Oct;28(10):1053-6. doi: 10.1038/nbt1010-1053.

16.

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis.

Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16927-32. doi: 10.1073/pnas.1316009110. Epub 2013 Sep 30.

17.

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR.

Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112. Epub 2013 Jun 5.

18.

Comparative epigenomics: defining and utilizing epigenomic variations across species, time-course, and individuals.

Xiao S, Cao X, Zhong S.

Wiley Interdiscip Rev Syst Biol Med. 2014 Sep-Oct;6(5):345-52. doi: 10.1002/wsbm.1274. Epub 2014 Jul 15. Review.

PMID:
25044241
19.

Epigenetic discordance at imprinting control regions in twins.

Ollikainen M, Craig JM.

Epigenomics. 2011 Jun;3(3):295-306. doi: 10.2217/epi.11.18. Review.

PMID:
22122339
20.

GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association.

Rentería ME, Coolen MW, Statham AL, Choi RS, Qu W, Campbell MJ, Smith S, Henders AK, Montgomery GW, Clark SJ, Martin NG, Medland SE.

Twin Res Hum Genet. 2013 Aug;16(4):767-81. doi: 10.1017/thg.2013.30. Epub 2013 Jun 3.

PMID:
23725790
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