Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding von Biddie, Simon C., John, Sam, Sabo, Pete J., Thurman, Robert E., Johnson, Thomas A., Schiltz, R. Louis, Miranda, Tina B., Sung, Myong-Hee, Trump, Saskia, Lightman, Stafford L., Vinson, Charles, Stamatoyannopoulos, John A., Hager, Gordon L.

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Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes von Stergachis, Andrew B., Neph, Shane, Reynolds, Alex, Humbert, Richard, Miller, Brady, Paige, Sharon L., Vernot, Benjamin, Cheng, Jeffrey B., Thurman, Robert E., Sandstrom, Richard, Haugen, Eric, Heimfeld, Shelly, Murry, Charles E., Akey, Joshua M., Stamatoyannopoulos, John A.

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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns von Hager, Gordon L, Stamatoyannopoulos, John A, John, Sam, Sabo, Peter J, Thurman, Robert E, Sung, Myong-Hee, Biddie, Simon C, Johnson, Thomas A

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BEDOPS: high-performance genomic feature operations von NEPH, Shane, KUEHN, M. Scott, SANDSTROM, Richard, HUMBERT, Richard, STAMATOYANNOPOULOS, John A, REYNOLDS, Alex P, HAUGEN, Eric, THURMAN, Robert E, JOHNSON, Audra K, RYNES, Eric, MAURANO, Matthew T, VIERSTRA, Jeff, THOMAS, Sean

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Topologically associating domains are stable units of replication-timing regulation von Pope, Benjamin D., Ryba, Tyrone, Dileep, Vishnu, Yue, Feng, Wu, Weisheng, Denas, Olgert, Vera, Daniel L., Wang, Yanli, Hansen, R. Scott, Canfield, Theresa K., Thurman, Robert E., Cheng, Yong, Gülsoy, Günhan, Dennis, Jonathan H., Snyder, Michael P., Stamatoyannopoulos, John A., Taylor, James, Hardison, Ross C., Kahveci, Tamer, Ren, Bing, Gilbert, David M.

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Widespread plasticity in CTCF occupancy linked to DNA methylation von Wang, Hao, Maurano, Matthew T, Qu, Hongzhu, Varley, Katherine E, Gertz, Jason, Pauli, Florencia, Lee, Kristen, Canfield, Theresa, Weaver, Molly, Sandstrom, Richard, Thurman, Robert E, Kaul, Rajinder, Myers, Richard M, Stamatoyannopoulos, John A

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An expansive human regulatory lexicon encoded in transcription factor footprints von Neph, Shane, Vierstra, Jeff, Stergachis, Andrew B., Reynolds, Alex P., Haugen, Eric, Vernot, Benjamin, Thurman, Robert E., John, Sam, Sandstrom, Richard, Johnson, Audra K., Maurano, Matthew T., Humbert, Richard, Rynes, Eric, Wang, Hao, Vong, Shinny, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Roach, Vaughn, Dunn, Douglas, Neri, Jun, Schafer, Anthony, Hansen, R. Scott, Kutyavin, Tanya, Giste, Erika, Weaver, Molly, Canfield, Theresa, Sabo, Peter, Zhang, Miaohua, Balasundaram, Gayathri, Byron, Rachel, MacCoss, Michael J., Akey, Joshua M., Bender, M. A., Groudine, Mark, Kaul, Rajinder, Stamatoyannopoulos, John A.

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Sequencing newly replicated DNA reveals widespread plasticity in human replication timing von Hansen, R. Scott, Thomas, Sean, Sandstrom, Richard, Canfield, Theresa K, Thurman, Robert E, Weaver, Molly, Dorschner, Michael O, Gartler, Stanley M, Stamatoyannopoulos, John A

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Global mapping of protein-DNA interactions in vivo by digital genomic footprinting von Stamatoyannopoulos, John A, Hesselberth, Jay R, Chen, Xiaoyu, Zhang, Zhihong, Sabo, Peter J, Sandstrom, Richard, Reynolds, Alex P, Thurman, Robert E, Neph, Shane, Kuehn, Michael S, Noble, William S, Fields, Stanley

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Conservation of trans-acting circuitry during mammalian regulatory evolution von Stergachis, Andrew B., Neph, Shane, Sandstrom, Richard, Haugen, Eric, Reynolds, Alex P., Zhang, Miaohua, Byron, Rachel, Canfield, Theresa, Stelhing-Sun, Sandra, Lee, Kristen, Thurman, Robert E., Vong, Shinny, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Dunn, Douglas, Vierstra, Jeff, Hansen, R. Scott, Johnson, Audra K., Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Treuting, Piper M., Kaul, Rajinder, Groudine, Mark, Bender, M. A., Borenstein, Elhanan, Stamatoyannopoulos, John A.

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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster von Karpen, Gary H, Park, Peter J, Kharchenko, Peter V, Alekseyenko, Artyom A, Schwartz, Yuri B, Minoda, Aki, Riddle, Nicole C, Ernst, Jason, Sabo, Peter J, Larschan, Erica, Gorchakov, Andrey A, Gu, Tingting, Linder-Basso, Daniela, Plachetka, Annette, Shanower, Gregory, Tolstorukov, Michael Y, Luquette, Lovelace J, Xi, Ruibin, Jung, Youngsook L, Park, Richard W, Bishop, Eric P, Canfield, Theresa P, Sandstrom, Richard, Thurman, Robert E, MacAlpine, David M, Stamatoyannopoulos, John A, Kellis, Manolis, Elgin, Sarah C. R, Kuroda, Mitzi I, Pirrotta, Vincenzo

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Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana von Sullivan, Alessandra M., Arsovski, Andrej A., Lempe, Janne, Bubb, Kerry L., Weirauch, Matthew T., Sabo, Peter J., Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Reynolds, Alex P., Stergachis, Andrew B., Vernot, Benjamin, Johnson, Audra K., Haugen, Eric, Sullivan, Shawn T., Thompson, Agnieszka, Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Mnaimneh, Sanie, Yang, Ally, Hughes, Timothy R., Nemhauser, Jennifer L., Queitsch, Christine, Stamatoyannopoulos, John A.

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Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair von Polak, Paz, Lawrence, Michael S, Haugen, Eric, Stoletzki, Nina, Stojanov, Petar, Thurman, Robert E, Garraway, Levi A, Mirkin, Sergei, Getz, Gad, Stamatoyannopoulos, John A, Sunyaev, Shamil R

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Nucleosome positioning signals in genomic DNA von Peckham, Heather E, Thurman, Robert E, Fu, Yutao, Stamatoyannopoulos, John A, Noble, William Stafford, Struhl, Kevin, Weng, Zhiping

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Predicting human nucleosome occupancy from primary sequence von Gupta, Shobhit, Dennis, Jonathan, Thurman, Robert E, Kingston, Robert, Stamatoyannopoulos, John A, Noble, William Stafford

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Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements von Hakim, Ofir, Sung, Myong-Hee, Voss, Ty C, Splinter, Erik, John, Sam, Sabo, Peter J, Thurman, Robert E, Stamatoyannopoulos, John A, de Laat, Wouter, Hager, Gordon L

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Nonfucosylation of an anti-TIGIT antibody enhances FcγR engagement, driving innate immune activation and antitumor activity von Smith, Alyson J, Thurman, Robert E, Zeng, Weiping, Grogan, Bryan, Lucas, Sasha, Gutierrez, Guadalupe, Heiser, Ryan A, Wo, Serena W, Blackmarr, Amber, Peterson, Scott, Gardai, Shyra J

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Identification of higher-order functional domains in the human ENCODE regions von Thurman, Robert E, Day, Nathan, Noble, William S, Stamatoyannopoulos, John A

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Unsupervised segmentation of continuous genomic data von Day, Nathan, Hemmaplardh, Andrew, Thurman, Robert E., Stamatoyannopoulos, John A., Noble, William S.

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Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques von Sullivan, Alessandra M., Arsovski, Andrej A., Thompson, Agnieszka, Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Johnson, Audra K., Sullivan, Shawn T., Sabo, Peter J., Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Nemhauser, Jennifer L., Stamatoyannopoulos, John A., Bubb, Kerry L., Queitsch, Christine

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