Discovery through epigenomics and informatics.

The Epigenome Center aims to enable new discovery methodologies employing massively parallel sequencing and other high-throughput technologies.

The Epigenome Center at Baylor College of Medicine participates in the NIH Epigenomics Roadmap Project. The aim of the NIH Epigenomics Roadmap project is to understand the variation of epigenomes (methylation status, histone marks, chromatin accessibility) across major tissue types and experimentally relevant cell lines and to detect and interpret epigenomic variation due to a selected set of developmental, physiological, and disease processes. The project will produce a Human Epigenome Atlas. The Atlas contains epigenomic maps of major tissue types and experimentally relevant cell lines.

About the Center

The Center's broad aim is to understand the variation of epigenomes (methylation status, histone marks, chromatin accessibility) across major human tissue types and experimentally relevant human cell lines and to detect and interpret epigenomic variation due to a selected set of developmental, physiological, and disease processes.

Center Members

Aleksandar Milosavljevic, Ph.D.Professor
Arthur E. Beaudet, M.D.Professor
Wei Li, Ph.D.Associate Professor
Robert Waterland, Ph.D.Associate Professor
Kjersti M. Aagaard-Tillery, M.D.Associate Professor

Andrew R. JacksonLead Programmer Analyst
Kevin RiehleLead Bioinformatics Programmer
Ronak PatelInstructor
Viren AminGraduate Student
Vitor OnuchicGraduate Student

Select Publications

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. joural: Science. 2018 361: 6409. Doi: 10:1126/science.aar3146.

Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel R, Rozowsky J, Galeev T, Huang Z, Altshuler R, Zhang Z, Harris R, Coarfa C, Ashmore L, Bertol J, Fakhouri W, Yu F, Kellis M, Gerstein M, and Milosavljevic A.
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

International Human Epigenome Consortium

Cell. doi: 10.1016/j.cell.2016.11.007 (2016)

PMID: 27863232
Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types

Onuchic V, Hartmaier RJ, Boone DN, Samuels ML, Patel RY, White WM, Garovic VD, Oesterreich S, Roth ME, Lee AV, Milosavljevic A.

Cell Rep. doi: 10.1016/j.celrep.2016.10.057 (2016)

PMID: 27851969
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

Amin V, Harris RA, Onuchic V, Jackson A, Charnecki T, Paithankar S, Subramanian S, Riehle K, Coarfa C, Milosavljevic A.

Nat. Commun. 6:6370 doi: 10.1038/ncomms7370 (2015)

PMID: 25691256
Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium et. al.

Nature doi: 10.1038/nature14248 (2015)

PMID: 25693563
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.

PMID: 25080362
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA.

Nucleic Acids Res. 2014 Apr;42(6):e43. doi: 10.1093/nar/gkt1325. Epub 2014 Jan 3.

PMID: 24391148
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
Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability

Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.

PLoS Genet. 2013;9(2):e1003333. doi: 10.1371/journal.pgen.1003333. Epub 2013 Feb 28. No abstract available.

PMID: 23468659
Spark: a navigational paradigm for genomic data exploration

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ.

Genome Res. 2012 Nov;22(11):2262-9. doi: 10.1101/gr.140665.112. Epub 2012 Sep 7.

PMID: 22960372
Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Saraj S, Dobson R, Schalkwyk LC, Mill J.

Genome Biol. 2012 Jun 15;13(6):R43. doi: 10.1186/gb-2012-13-6-r43.

PMID: 22703893
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.

PLoS Genet. 2012;8(5):e1002692. doi: 10.1371/journal.pgen.1002692. Epub 2012 May 17.

PMID: 22615578
Emerging patterns of epigenomic variation

Milosavljevic A

Trends in Genetics, 2011 Jun;27(6):242-50

PMID: 21507501
Putting epigenome comparison into practice

Milosavljevic A

Nat Biotechnol., 2010 Oct;28(10):1053-6

PMID: 20944597
The NIH Roadmap Epigenomics Mapping Consortium

Bernstein BE, Stamatoyannopoulus JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

Nat Biotechnol., 2010 Oct;28(10):1045-8

PMID: 20944595
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

PMID: 20852635

Discovery through epigenomics and informatics.

The Epigenome Center aims to enable new discovery methodologies employing massively parallel sequencing and other high-throughput technologies.

About the Center

NIH Roadmap Epigenomics Project

Genboree

Epigenome Atlas

Center Members

Select Publications

Funding

We gratefully acknowledges the generous support:

EPIGENOME CENTER