Large-scale discovery and validation of functional elements in the human genome by Kellis, Manolis, Bernstein, Bradley E.

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Development and validation of a T7 based linear amplification for genomic DNA by Schreiber Stuart L, Liu Chih Long, Bernstein Bradley E

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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

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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

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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.

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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.

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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.

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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.

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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.

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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

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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

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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.

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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.

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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

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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.

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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.

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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.

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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-

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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

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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.

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