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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Fold-specific substitution matrices for protein classification von Vilim, R. B., Cunningham, R. M., Lu, B., Kheradpour, P., Stevens, F. J.

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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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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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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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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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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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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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Comparative analysis of regulatory information and circuits across distant species von Boyle, Alan P., Araya, Carlos L., Brdlik, Cathleen, Cayting, Philip, Cheng, Chao, Cheng, Yong, Gardner, Kathryn, Hillier, LaDeana W., Janette, Judith, Jiang, Lixia, Kasper, Dionna, Kawli, Trupti, Kheradpour, Pouya, Kundaje, Anshul, Li, Jingyi Jessica, Ma, Lijia, Niu, Wei, Rehm, E. Jay, Rozowsky, Joel, Slattery, Matthew, Spokony, Rebecca, Terrell, Robert, Vafeados, Dionne, Wang, Daifeng, Weisdepp, Peter, Wu, Yi-Chieh, Xie, Dan, Yan, Koon-Kiu, Feingold, Elise A., Good, Peter J., Pazin, Michael J., Huang, Haiyan, Bickel, Peter J., Brenner, Steven E., Reinke, Valerie, Waterston, Robert H., Gerstein, Mark, White, Kevin P., Kellis, Manolis, Snyder, Michael

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Sharing and Specificity of Co-expression Networks across 35 Human Tissues von Pierson, Emma, Koller, Daphne, Battle, Alexis, Mostafavi, Sara, Ardlie, Kristin G, Getz, Gad, Wright, Fred A, Kellis, Manolis, Volpi, Simona, Dermitzakis, Emmanouil T

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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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Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster von Slattery, Matthew, Ma, Lijia, Spokony, Rebecca F, Arthur, Robert K, Kheradpour, Pouya, Kundaje, Anshul, Nègre, Nicolas, Crofts, Alex, Ptashkin, Ryan, Zieba, Jennifer, Ostapenko, Alexander, Suchy, Sarah, Victorsen, Alec, Jameel, Nader, Grundstad, A Jason, Gao, Wenxuan, Moran, Jennifer R, Rehm, E Jay, Grossman, Robert L, Kellis, Manolis, White, Kevin P

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Corrigendum: 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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Correction: Corrigendum: 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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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, Argmann, Carmen, Zhao, Yong, Zhu, Jun, Tu, Zhidong, Ardlie, Kristin G, Deluca, David S, Segrè, Ayellet V, Sullivan, Timothy J, Young, Taylor R, Gelfand, Ellen T, Trowbridge, Casandra A, Maller, Julian B, Tukiainen, Taru, Lek, Monkol, Ward, Lucas D, Kheradpour, Pouya, Iriarte, Benjamin, Meng, Yan, Palmer, Cameron D, Winckler, Wendy, Hirschhorn, Joel, MacArthur, Daniel G, Shablin, Andrey A, Li, Gen, Zhou, Yi-Hui, Rusyn, Ivan, Lappalainen, Tuuli, Ongen, Halit, Rivas, Manuel A, Battle, Alexis, Sammeth, Michael, Mele, Marta, Reverter, Ferran, Goldman, Jakob, Guigo, Roderic, Dermitzakis, Emmanouil T, Konkashbaev, Anuar, Nicolae, Dan L, Cox, Nancy J, Flutre, Timothée, Wen, Xiaoquan, Stephens, Matthew, Pritchard, Jonathan K, Lin, Luan, Liu, Jun, Mestichelli, Bernadette, Tidwell, Denee, Salvatore, Mike, Thomas, Jeffrey A, Lonsdale, John T, Karasik, Ellen, Ramsey, Kimberly, Moser, Michael T, Gillard, Bryan M, Fleming, Johnelle, Magazine, Harold, Hasz, Rick, Walters, Gary D, Miklos, Mark, Sullivan, Susan, Traino, Heather, Valley, Dana R, Rohrer, Daniel C, Jewel, Scott, Branton, Philip, Qi, Liqun, Hariharan, Pushpa, Tabor, David, Shive, Charles, Smith, Anna M, Buia, Stephen A, Undale, Anita H, Robinson, Karna L, Burges, Robin, Hambright, Kenneth W, Seleski, John, Korzeniewski, Greg E, Marcus, Yvonne, Tejada, Jorge, Taherian, Mehran, Lu, Chunrong, Robles, Barnaby E, Basile, Margaret, Mash, Deborah C, Volpi, Simona, Struewing, Jeff, Temple, Gary F, Boyer, Joy, Colantuoni, Deborah, Carithers, NCI Latarsha J, Guan, Ping, Compton, Carolyn, Demchok, Joanne P, Vaught, Jimmie B, Rabiner, Chana A, Lockhart, Nicole C

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Secondary Precursor T-Cell Lymphoblastic Lymphoma Following Precursor B-cell Acute Lymphoblastic Leukemia: A Case Report and Review of the Literature von Jenny L. Smith, Albert Kheradpour, Craig W. Zuppan, Jun Wang, Rhett P. Ketterling, Edward H. Rowsell

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Outcomes of Measurable Residual Disease in Pediatric Acute Myeloid Leukemia before and after Hematopoietic Stem Cell Transplant: Validation of Difference from Normal Flow Cytometry... von Jacobsohn, David A., Loken, Michael R., Fei, Mingwei, Adams, Alexia, Brodersen, Lisa Eidenschink, Logan, Brent R., Ahn, Kwang Woo, Shaw, Bronwen E., Kletzel, Morris, Olszewski, Marie, Khan, Sana, Meshinchi, Soheil, Keating, Amy, Harris, Andrew, Teira, Pierre, Duerst, Reggie E., Margossian, Steven P., Martin, Paul L., Petrovic, Aleksandra, Dvorak, Christopher C., Nemecek, Eneida R., Boyer, Michael W., Chen, Allen R., Davis, Jeffrey H., Shenoy, Shalini, Savasan, Sureyya, Hudspeth, Michelle P., Adams, Roberta H., Lewis, Victor A., Kheradpour, Albert, Kasow, Kimberly A., Gillio, Alfred P., Haight, Ann E., Bhatia, Monica, Bambach, Barbara J., Haines, Hilary L., Quigg, Troy C., Greiner, Robert J., Talano, Julie-An M., Delgado, David C., Cheerva, Alexandra, Gowda, Madhu, Ahuja, Sanjay, Ozkaynak, Mehmet, Mitchell, David, Schultz, Kirk R., Fry, Terry J., Loeb, David M., Pulsipher, Michael A.

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Amplification of the Dihydrofolate Reductase Gene Is a Mechanism of Acquired Resistance to Methotrexate in Patients With Acute Lymphoblastic Leukemia and Is Correlated With p53 Gen... von Göker, Erdem, Waltham, Mark, Kheradpour, Albert, Trippett, Tanya, Mazumdar, Madhu, Elisseyeff, Yaroslav, Schnieders, Barbara, Steinherz, Peter, Tan, Charlotte, Berman, Ellin, Bertino, Joseph R.

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