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

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

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