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ENCODE Project - BroadE

In May 2020, the Epigenomics team partnered with the BroadE Workshop Series to present the second annual, virtual version of the ENCODE Data Utilization Workshop. In this four-part recording of the workshop, you'll learn how to access and work with data via both the ENCODE portal and Search Candidate cis-Regulatory Elements by ENCODE (SCREEN) from leaders from the National Human Genome Research Institute and Broad’s partners at the Stanford ENCODE data coordination center and the University of Massachusetts data analysis center. Check it out!

View the the YouTube playlist of the four presentations

Seminar series

The Cell Circuits & Epigenomics programs host a weekly seminar series at the Broad Institute for affiliated members on anything and everything to do with genome biology and cell circuitry. If you would like to be added to the distribution list, please email

Check out and share our growing library of Cell Circuits & Epigenomics Primers:

Michael Bronstein: “Geometric Deep Learning for Function Protein Design” from April 6, 2020.
Michael Bronstein is a professor at Imperial College London and University of Lugano and Head of Graph Learning Research at Twitter.

Travis Hughes: “Seq-Well: A portable, low cost platform for single-cell RNA-sequencing of low input samples”

Anne Carpenter: “The Broad Imaging Platform”


Learn more about the epigenome

Five questions for Brad Bernstein
Brad Bernstein answered five questions posed by the BroadMinded blog about epigenomics and his work to develop a high-sensitivity form of Chip-Seq.

Brad Bernstein explains the epigenome
In this BroadView video, Epigenomics Program director Brad Bernstein explains the epigenome and the role it plays in cancer development.


Research news from the Epigenomics Program

Deciphering chromatin: Many marks, millions of histones at a time
A new high-resolution technique for reading combinations of chemical flags in the epigenome, reported in Science, could help uncover new rules underlying cell fate and provide important clues for understanding diseases like cancer.

Enhancer hijacking means a power-up for salivary gland cancer
In Nature Genetics, Yotam Drier, Birgit Knoechel, Brad Bernstein, and other colleagues, explore the implications of a special kind of translocation — one that repositions an oncogene, its promoter, and a nearby super-enhancer as a single unit — in adenoid cystic carcinoma.

For drivers of Alzheimer’s disease, check the roadmap
To understand the impact of gene regulation in Alzheimer’s disease (AD), a team of researchers led by Manolis Kellis mapped the epigenetic landscape of AD-associated neurodegeneration, reporting their findings in Nature.

Glioblastoma’s “stem-like” cells laid bare
In a paper in Cell, a team led by Mario Suva, Esther Rheinbay, and Brad Bernstein described a network of genes controlled in glioblastoma by four transcription factors, as well as insights into potential therapeutic strategies.

Insights into drug resistance for a rare leukemia
A team led by Brigit Knoechel and Brad Bernstein report in Nature Genetics that an epigenetic factor, BRD4, plays a crucial role in the ability of T-cell acute lymphoblastic leukemia (T-ALL) cells to resist treatment with NOTCH1 inhibitors.

Editing the epigenome
A team of researchers from the Epigenomics Program and MGH reported in Nature Biotechnology their efforts to develop a TAL effector-based method to test the functions of suspected enhancers by homing in on their signature epigenomic marks.

Rewinding the clock with epigenomics
In a review article in Science, Brad Bernstein, Mario Suvà, and Nicolo Riggi describe deep insights gained about features shared between oncogenesis, induced pluripotency, and directed differentiation.

Epigenomics approach illuminates the dark corners of the genome
Broad researchers described in Nature Biotechnology the use of a computational technique to predict the function in some of the non-coding parts of the genome in human T cells.

The machinery of chromatin regulation
Oren Ram, Alon Goren, Aviv Regev, Brad Bernstein, and colleagues reveal in Cell that specific combinations of chromatin regulator proteins control essential chromatin activities, like histone modification.

Broad Institute awarded major grant to bolster epigenomics research
The Epigenomics Program received a five-year, ~$15 million grant designating the institute to become one of four NIH Roadmap for Medical Research Reference Epigenome Mapping Center nationwide.

Gaining ground on glioblastoma
Certain regulatory proteins play a major role in the “self-renewing” cancer stem cells that drive glioblastoma growth, according to research published in Cell Reports by Esther Rheinbay, Mario L. Suvà, Brad Bernstein, and colleagues.

Broad epigenetics research makes a big splash
An analysis of four methylation mapping approaches revealed that the four methods all produce accurate DNA methylation data, but differ in the ability to detect regions that are methylated differently.