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Chuck Epstein

Ryan RJ, et al. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov. 2015 Oct;5(10):1058-71.

Farh KKH, Marson A, Zhu J, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015;518(7539):337–343.

Ernst J, Kheradpour P, Mikkelsen T, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Epub 2011 Mar 23.

Ram O, Goren A, Amit I, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec:147(7):1628-39.

Chuck Epstein, Ph.D.

Chuck Epstein is an expert at the characterization of the state of the epigenome of rare and low abundance mammalian cells, and he aspires to collaborate in harnessing the power of epigenome characterization for disease stratification and the selection and development of optimal therapeutics. Epstein is a senior group leader in the Broad’s Epigenomics Program, which characterizes chromatin structure and histone modifications in a diverse range of cell types. These modifications affect gene expression and play a crucial role in cellular differentiation during development, and their dysregulation can be a key driver of drug resistance and disease.

Epstein has been responsible for coordinating the Broad’s contributions to NIH-funded consortia in the realm of epigenomics (ENCODE II, ENCODE III, and NIH Roadmap Epigenomics), as well as to diverse studies of the epigenome in cancer. To enable these large-scale projects, Epstein has coordinated the efforts of a laboratory team and a computational team, helping ensure that the program’s computational infrastructure meets the requirements of consortium-scale data generation. He has worked closely with computational biologists to develop innovative methods to ensure data quality.

Epstein has also overseen technology development related to the ChIP-seq method and is currently directly involved in technology development as the principal investigator of an internal SPARC grant. He has served the Broad as an inaugural member of the Staff Scientist Development Committee and as a mentor to summer students, and is currently a co-organizer of the Cell Circuits and Epigenomics Seminar Series.

Epstein joined the Broad in July 2008 after working as principal research investigator (focused on transcript profiling for biomarker discovery) with Sanofi-Aventis Pharmaceuticals. Prior to that, he completed his Ph.D. with Fred Cross at The Rockefeller University and conducted postdoctoral research as a Damon-Runyon Fellow with Arnold Levine (Princeton) and Ron Butow (Southwestern Medical Center).

Contact Chuck Epstein via email at

June 2016