Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments von Kheradpour, Pouya, Kellis, Manolis

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Mapping and analysis of chromatin state dynamics in nine human cell types von Ernst, Jason, Kheradpour, Pouya, Mikkelsen, Tarjei S., Shoresh, Noam, Ward, Lucas D., Epstein, Charles B., Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael, Ku, Manching, Durham, Timothy, Kellis, Manolis, Bernstein, Bradley E.

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Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay von Kheradpour, Pouya, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei S, Kellis, Manolis

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Evidence of reduced recombination rate in human regulatory domains von Liu, Yaping, Sarkar, Abhishek, Kheradpour, Pouya, Ernst, Jason, Kellis, Manolis

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Reliable prediction of regulator targets using 12 Drosophila genomes von Kheradpour, Pouya, Stark, Alexander, Roy, Sushmita, Kellis, Manolis

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Histone modifications at human enhancers reflect global cell-type-specific gene expression von Ren, Bing, Heintzman, Nathaniel D, Hon, Gary C, Hawkins, R. David, Kheradpour, Pouya, Stark, Alexander, Harp, Lindsey F, Ye, Zhen, Lee, Leonard K, Stuart, Rhona K, Ching, Christina W, Ching, Keith A, Antosiewicz-Bourget, Jessica E, Liu, Hui, Zhang, Xinmin, Green, Roland D, Lobanenkov, Victor V, Stewart, Ron, Thomson, James A, Crawford, Gregory E, Kellis, Manolis

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Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets von Guo, Michael H, Sama, Prashanth, LaBarre, Brenna A, Lokhande, Hrishikesh, Balibalos, John, Chu, Ci, Du, Xiaomi, Kheradpour, Pouya, Kim, Charles C, Oniskey, Taylor, Snyder, Thomas, Soghoian, Damien Z, Weiner, Howard L, Chitnis, Tanuja, Patsopoulos, Nikolaos A

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A comprehensive map of insulator elements for the Drosophila genome von Nègre, Nicolas, Brown, Christopher D, Shah, Parantu K, Kheradpour, Pouya, Morrison, Carolyn A, Henikoff, Jorja G, Feng, Xin, Ahmad, Kami, Russell, Steven, White, Robert A H, Stein, Lincoln, Henikoff, Steven, Kellis, Manolis, White, Kevin P

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Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes von Stark, Alexander, Kheradpour, Pouya, Parts, Leopold, Brennecke, Julius, Hodges, Emily, Hannon, Gregory J, Kellis, Manolis

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A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands von Stark, Alexander, Bushati, Natascha, Jan, Calvin H, Kheradpour, Pouya, Hodges, Emily, Brennecke, Julius, Bartel, David P, Cohen, Stephen M, Kellis, Manolis

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Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer von Murchison, Elizabeth P, Tovar, Cesar, Hsu, Arthur, Bender, Hannah S, Kheradpour, Pouya, Rebbeck, Clare A, Obendorf, David, Conlan, Carly, Bahlo, Melanie, Blizzard, Catherine A, Pyecroft, Stephen, Kreiss, Alexandre, Kellis, Manolis, Stark, Alexander, Harkins, Timothy T, Graves, Jennifer A. Marshall, Woods, Gregory M, Hannon, Gregory J, Papenfuss, Anthony T

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Early immune factors associated with the development of post-acute sequelae of SARS-CoV-2 infection in hospitalized and non-hospitalized individuals von Leung, Jacqueline M, Wu, Michelle J, Kheradpour, Pouya, Chen, Chen, Drake, Katherine A, Tong, Gary, Ridaura, Vanessa K, Zisser, Howard C, Conrad, William A, Hudson, Natalia, Allen, Jared, Welberry, Christopher, Parsy-Kowalska, Celine, Macdonald, Isabel, Tapson, Victor F, Moy, James N, deFilippi, Christopher R, Rosas, Ivan O, Basit, Mujeeb, Krishnan, Jerry A, Parthasarathy, Sairam, Prabhakar, Bellur S, Salvatore, Mirella, Kim, Charles C

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Conservation of small RNA pathways in platypus von Murchison, Elizabeth P, Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, Kellis, Manolis, Grützner, Frank, Stark, Alexander, Hannon, Gregory J

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Integrative analysis of 111 reference human epigenomes von Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Bilenky, Misha, Yen, Angela, Heravi-Moussavi, Alireza, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ziller, Michael J., Amin, Viren, Whitaker, John W., Schultz, Matthew D., Ward, Lucas D., Sarkar, Abhishek, Quon, Gerald, Sandstrom, Richard S., Eaton, Matthew L., Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Coarfa, Cristian, Harris, R. Alan, Shoresh, Noam, Epstein, Charles B., Gjoneska, Elizabeta, Leung, Danny, Xie, Wei, Hawkins, R. David, Lister, Ryan, Hong, Chibo, Gascard, Philippe, Mungall, Andrew J., Moore, Richard, Chuah, Eric, Tam, Angela, Canfield, Theresa K., Hansen, R. Scott, Kaul, Rajinder, Sabo, Peter J., Bansal, Mukul S., Carles, Annaick, Dixon, Jesse R., Farh, Kai-How, Feizi, Soheil, Karlic, Rosa, Kim, Ah-Ram, Kulkarni, Ashwinikumar, Li, Daofeng, Lowdon, Rebecca, Elliott, GiNell, Mercer, Tim R., Neph, Shane J., Onuchic, Vitor, Polak, Paz, Rajagopal, Nisha, Ray, Pradipta, Sallari, Richard C., Siebenthall, Kyle T., Sinnott-Armstrong, Nicholas A., Stevens, Michael, Thurman, Robert E., Wu, Jie, Zhang, Bo, Zhou, Xin, Beaudet, Arthur E., Boyer, Laurie A., De Jager, Philip L., Farnham, Peggy J., Fisher, Susan J., Haussler, David, Jones, Steven J. M., Li, Wei, Marra, Marco A., McManus, Michael T., Sunyaev, Shamil, Thomson, James A., Tlsty, Thea D., Tsai, Li-Huei, Wang, Wei, Waterland, Robert A., Zhang, Michael Q., Chadwick, Lisa H., Bernstein, Bradley E., Costello, Joseph F., Ecker, Joseph R., Hirst, Martin, Meissner, Alexander, Milosavljevic, Aleksandar, Ren, Bing, Stamatoyannopoulos, John A., Wang, Ting, Kellis, Manolis

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia von Landt, Stephen G, Marinov, Georgi K, Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E, Bickel, Peter, Brown, James B, Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I, Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J, Hoffman, Michael M, Iyer, Vishwanath R, Jung, Youngsook L, Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V, Li, Qunhua, Liu, Tao, Liu, X Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M, Park, Peter J, Pazin, Michael J, Perry, Marc D, Raha, Debasish, Reddy, Timothy E, Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A, Tolstorukov, Michael Y, White, Kevin P, Xi, Simon, Farnham, Peggy J, Lieb, Jason D, Wold, Barbara J, Snyder, Michael

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE von Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V, Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L, Landolin, Jane M, Bristow, Christopher A, Ma, Lijia, Lin, Michael F, Washietl, Stefan, Arshinoff, Bradley I, Ay, Ferhat, Meyer, Patrick E, Robine, Nicolas, Washington, Nicole L, Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D, Candeias, Rogerio, Carlson, Joseph W, Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y, Will, Sebastian, Alekseyenko, Artyom A, Artieri, Carlo, Booth, Benjamin W, Brooks, Angela N, Dai, Qi, Davis, Carrie A, Duff, Michael O, Feng, Xin, Gorchakov, Andrey A, Gu, Tingting, Henikoff, Jorja G, Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K, Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K, Riddle, Nicole C, Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E, Schwartz, Yuri B, Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H, Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E, Brent, Michael R, Cherbas, Lucy, Elgin, Sarah C.R, Gingeras, Thomas R, Grossman, Robert, Hoskins, Roger A, Kaufman, Thomas C, Kent, William, Kuroda, Mitzi I, Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W, Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R, Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J, Celniker, Susan E, Henikoff, Steven, Karpen, Gary H, Lai, Eric C, MacAlpine, David M, Stein, Lincoln D, White, Kevin P, Kellis, Manolis

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An Epigenetic Signature for Monoallelic Olfactory Receptor Expression von Magklara, Angeliki, Yen, Angela, Colquitt, Bradley M., Clowney, E. Josephine, Allen, William, Markenscoff-Papadimitriou, Eirene, Evans, Zoe A., Kheradpour, Pouya, Mountoufaris, George, Carey, Catriona, Barnea, Gilad, Kellis, Manolis, Lomvardas, Stavros

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A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project von Carithers, Latarsha J, Ardlie, Kristin, Barcus, Mary, Branton, Philip A, Britton, Angela, Buia, Stephen A, Compton, Carolyn C, DeLuca, David S, Peter-Demchok, Joanne, Gelfand, Ellen T, Guan, Ping, Korzeniewski, Greg E, Lockhart, Nicole C, Rabiner, Chana A, Rao, Abhi K, Robinson, Karna L, Roche, Nancy V, Sawyer, Sherilyn J, Segrè, Ayellet V, Shive, Charles E, Smith, Anna M, Sobin, Leslie H, Undale, Anita H, Valentino, Kimberly M, Vaught, Jim, Young, Taylor R, Moore, Helen M

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A cis-regulatory map of the Drosophila genome von Nègre, Nicolas, Brown, Christopher D., Ma, Lijia, Bristow, Christopher Aaron, Miller, Steven W., Wagner, Ulrich, Kheradpour, Pouya, Eaton, Matthew L., Loriaux, Paul, Sealfon, Rachel, Li, Zirong, Ishii, Haruhiko, Spokony, Rebecca F., Chen, Jia, Hwang, Lindsay, Cheng, Chao, Auburn, Richard P., Davis, Melissa B., Domanus, Marc, Shah, Parantu K., Morrison, Carolyn A., Zieba, Jennifer, Suchy, Sarah, Senderowicz, Lionel, Victorsen, Alec, Bild, Nicholas A., Grundstad, A. Jason, Hanley, David, MacAlpine, David M., Mannervik, Mattias, Venken, Koen, Bellen, Hugo, White, Robert, Gerstein, Mark, Russell, Steven, Grossman, Robert L., Ren, Bing, Posakony, James W., Kellis, Manolis, White, Kevin P.

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Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases von Yang, Jialiang, Huang, Tao, Petralia, Francesca, Long, Quan, Zhang, Bin, Argmann, Carmen, Zhao, Yong, Mobbs, Charles V., Schadt, Eric E., Zhu, Jun, Tu, Zhidong

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