Large-scale discovery and validation of functional elements in the human genome

by Kellis, Manolis, Bernstein, Bradley E.
Published 2010

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

by Qi, Yifeng, Reyes, Alejandro, Johnstone, Sarah E., Aryee, Martin J., Bernstein, Bradley E., Zhang, Bin
Published 2022

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

by Qi, Yifeng, Reyes, Alejandro, Johnstone, Sarah E, Aryee, Martin J, Bernstein, Bradley E, Zhang, Bin
Published 2022

Digital transcriptome profiling from attomole-level RNA samples

by Ozsolak, Fatih, Goren, Alon, Gymrek, Melissa A., Guttman, Mitchell, Regev, Aviv, Bernstein, Bradley E., Milos, Patrice M.
Published 2012

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

by Ku, Manching, Jaffe, Jacob D., Koche, Richard Patrick, Rheinbay, Esther, Endoh, Mitsuhiro, Koseki, Haruhiko, Carr, Steven A., Bernstein, Bradley E.
Published 2013

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

by Ku, Manching, Rheinbay, Esther, Endoh, Mitsuhiro, Koseki, Haruhiko, Koche, Richard Patrick, Jaffe, Jacob D., Carr, Steven A., Bernstein, Bradley E.
Published 2012

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

by Mendenhall, Eric M., Koche, Richard Patrick, Truong, Thanh, Zhou, Vicky W., Issac, Biju, Chi, Andrew S., Ku, Manching, Bernstein, Bradley E.
Published 2011

Model-based Analysis of ChIP-Seq (MACS)

by Zhang, Yong, Liu, Tao, Meyer, Clifford A., Eeckhoute, Jerome, Johnson, David S., Nusbaum, Chad, Myers, Richard M., Brown, Myles, Li, Wei, Liu, Xiaole S., Bernstein, Bradley E.
Published 2010

Wilms Tumor Chromatin Profiles Highlight Stem Cell Properties and a Renal Developmental Network

by Aiden, Aviva Presser, Rivera, Miguel N., Rheinbay, Esther, Ku, Manching, Coffman, Erik J., Truong, Thanh T., Vargas, Sara O., Haber, Daniel A., Bernstein, Bradley E., Lander, Eric Steven
Published 2012

Systematic dissection of genomic features determining transcription factor binding and enhancer function

by Zhang, Xiaolan, Wang, Li, Melnikov, Alexandre, Rogov, Peter, Tewhey, Ryan, Isakova, Alina, Deplancke, Bart, Bernstein, Bradley E., Mikkelsen, Tarjei S., Grossman, Sharon Rachel, Engreitz, Jesse Michael, Lander, Eric Steven
Published 2017

The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism

by Zwaans, Bernadette M.M, Silberman, Dafne M, Goren, Alon, Zhong, Lei, Ram, Oren, Truelove, Jessica, Guimaraes, Alexander R., Toiber, Debra, Cosentino, Claudia, Greenson, Joel K, MacDonald, Alasdair I, McGlynn, Liane, Maxwell, Fraser, Edwards, Joanne, Giacosa, Sofia, Guccione, Ernesto, Weissleder, Ralph, Bernstein, Bradley E., Regev, Aviv, Shiels, Paul G, Lombard, David B., Mostoslavsky, Raul, Sebastian, Carlos, Gymrek, Melissa A., Bernstein, Bradley E.
Published 2014

Insights into GATA-1 Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

by Yu, Ming, Riva, Laura, Schindler, Yocheved, Moran, Tyler B., Cheng, Yong, Yu, Duonan, Hardison, Ross C., Weiss, Mitchell J., Orkin, Stuart H., Bernstein, Bradley E., Fraenkel, Ernest, Cantor, Alan B.
Published 2010

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

by Presser, Aviva, Guttman, Mitchell, Raj, Arjun, van Oudenaarden, Alexander, Rinn, John L., Lander, Eric S., Regev, Aviv, Bernstein, Bradley E., Thomas, Kelly, Morales, Dianali Rivea, Garber, Manuel, Khalil, Ahmad M., Huarte, Maite
Published 2010

Mapping and Analysis of Chromatin State Dynamics in Nine Human Cell Types

by Ernst, Jason, Kheradpour, Pouya, Mikkelsen, Tarjei Sigurd, Shoresh, Noam, Ward, Lucas D., Epstein, Charles B., Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Ku, Manching, Durham, Timothy, Kellis, Manolis, Bernstein, Bradley E.
Published 2012

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

by Ram, Oren, Goren, Alon, Amit, Ido, Shoresh, Noam, Yosef, Nir, Ernst, Jason, Kellis, Manolis, Issner, Robbyn, Durham, Timothy, Zhang, Xiaolan, Donaghey, Julie, Epstein, Charles B., Regev, Aviv, Bernstein, Bradley E., Gymrek, Melissa A., Coyne, Michael J.
Published 2014

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

by Patel, A. P., Tirosh, I., Trombetta, J. J., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., Louis, D. N., Rozenblatt-Rosen, O., Suva, M. L., Bernstein, Bradley E., Regev, Aviv, Shalek, Alex K.
Published 2015

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

by Bernstein, Bradley E., Epstein, Charles B., Shoresh, Noam, Ernst, Jason, Mikkelsen, Tarjei Sigurd, Kheradpour, Pouya, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Ward, Lucas D., Altshuler, Robert Charles, Lin, Michael F., Kellis, Manolis, ENCODE Project Consortium
Published 2011

Chromatin Signature Reveals over a Thousand Highly Conserved Large Non-Coding Rnas in Mammals

by Guttman, Mitchell, Amit, Ido, Garber, Manuel, French, Courtney, Lin, Michael F., Feldser, David M., Huarte, Maite, Zuk, Or, Carey, Bryce W., Cassady, John P., Cabili, Moran N., Jaenisch, Rudolf, Jacks, Tyler E., Hacohen, Nir, Bernstein, Bradley E., Kellis, Manolis, Lander, Eric S., Mikkelsen, Tarjei Sigurd 1978-
Published 2010

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

by Puram, Sidharth V., Tirosh, Itay, Parikh, Anuraag S., Patel, Anoop P., Yizhak, Keren, Gillespie, Shawn, Rodman, Christopher, Luo, Christina L., Mroz, Edmund A., Emerick, Kevin S., Deschler, Daniel G., Varvares, Mark A., Mylvaganam, Ravi, Rozenblatt-Rosen, Orit, Rocco, James W., Faquin, William C., Lin, Derrick T., Regev, Aviv, Bernstein, Bradley E.
Published 2018