Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

by Kheradpour, Pouya, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei S, Kellis, Manolis
Published in Genome research

Fold-specific substitution matrices for protein classification

by Vilim, R. B., Cunningham, R. M., Lu, B., Kheradpour, P., Stevens, F. J.
Published in Bioinformatics

A comprehensive map of insulator elements for the Drosophila genome

by 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
Published in PLoS genetics

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

by Stark, Alexander, Bushati, Natascha, Jan, Calvin H, Kheradpour, Pouya, Hodges, Emily, Brennecke, Julius, Bartel, David P, Cohen, Stephen M, Kellis, Manolis
Published in Genes & development

Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer

by 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
Published in Science (American Association for the Advancement of Science)

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

by 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
Published in Genome research

A cis-regulatory map of the Drosophila genome

by NEGRE, Nicolas, BROWN, Christopher D, ZIRONG LI, ISHII, Haruhiko, SPOKONY, Rebecca F, JIA CHEN, HWANG, Lindsay, CHAO CHENG, AUBURN, Richard P, DAVIS, Melissa B, DOMANUS, Marc, SHAH, Parantu K, LIJIA MA, MORRISON, Carolyn A, ZIEBA, Jennifer, SUCHY, Sarah, SENDEROWICZ, Lionel, VICTORSEN, Alec, BILD, Nicholas A, GRUNDSTAD, A. Jason, HANLEY, David, MACALPINE, David M, MANNERVIK, Mattias, AARON BRISTOW, Christopher, VENKEN, Koen, BELLEN, Hugo, WHITE, Robert, GERSTEIN, Mark, RUSSELL, Steven, GROSSMAN, Robert L, BING REN, POSAKONY, James W, KELLIS, Manolis, WHITE, Kevin P, MILLER, Steven W, WAGNER, Ulrich, KHERADPOUR, Pouya, EATON, Matthew L, LORIAUX, Paul, SEALFON, Rachel
Published in Nature (London)

Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

by Yang, Jialiang, Huang, Tao, Petralia, Francesca, Long, Quan, Zhang, Bin, Argmann, Carmen, Zhao, Yong, Mobbs, Charles V, Schadt, Eric E, Zhu, Jun, Tu, Zhidong
Published in Scientific reports

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

by Pierson, Emma, Koller, Daphne, Battle, Alexis, Mostafavi, Sara, Ardlie, Kristin G, Getz, Gad, Wright, Fred A, Kellis, Manolis, Volpi, Simona, Dermitzakis, Emmanouil T
Published in PLoS computational biology

Comparative analysis of regulatory information and circuits across distant species

by 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
Published in Nature (London)

Conservation of small RNA pathways in platypus

by Murchison, Elizabeth P, Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, Kellis, Manolis, Grützner, Frank, Stark, Alexander, Hannon, Gregory J
Published in Genome Research

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

by 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
Published in Genome research

Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

by Yang, Jialiang, Huang, Tao, Petralia, Francesca, Long, Quan, Zhang, Bin, Argmann, Carmen, Zhao, Yong, Mobbs, Charles V, Schadt, Eric E, Zhu, Jun, Tu, Zhidong
Published in Scientific reports

Correction: Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

by Yang, Jialiang, Huang, Tao, Petralia, Francesca, Zhang, Bin, Argmann, Carmen, Mobbs, Charles V., Schadt, Eric E., Zhu, Jun, Deluca, David S., Segrè, Ayellet V., Sullivan, Timothy J., Gelfand, Ellen T., Maller, Julian B., Tukiainen, Taru, Lek, Monkol, Ward, Lucas D., Iriarte, Benjamin, Palmer, Cameron D., Winckler, Wendy, Kellis, Manolis, MacArthur, Daniel G., Shablin, Andrey A., Li, Gen, Zhou, Yi-Hui, Nobel, Andrew B., Rusyn, Ivan, Wright, Fred A., Lappalainen, Tuuli, Ferreira, Pedro G., Rivas, Manuel A., Battle, Alexis, Monlong, Jean, Sammeth, Michael, Reverter, Ferran, Goldmann, Jakob, Koller, Daphne, Guigo, Roderic, McCarthy, Mark I., Dermitzakis, Emmanouil T., Konkashbaev, Anuar, Nicolae, Dan L., Flutre, Timothée, Wen, Xiaoquan, Stephens, Matthew, Pritchard, Jonathan K., Lin, Luan, Liu, Jun, Brown, Amanda, Tidwell, Denee, Lo, Edmund, Salvatore, Mike, Thomas, Jeffrey A., Lonsdale, John T., Choi, Christopher, Karasik, Ellen, Ramsey, Kimberly, Moser, Michael T., Gillard, Bryan M., Syron, John, Fleming, Johnelle, Magazine, Harold, Walters, Gary D., Bridge, Jason P., Miklos, Mark, Sullivan, Susan, Barker, Laura K., Traino, Heather, Mosavel, Magboeba, Valley, Dana R., Rohrer, Daniel C., Jewel, Scott, Branton, Philip, Sobin, Leslie H., Qi, Liqun, Wu, Shenpei, Tabor, David, Smith, Anna M., Buia, Stephen A., Undale, Anita H., Roche, Nancy, Britton, Angela, Burges, Robin, Seleski, John, Korzeniewski, Greg E., Erickson, Kenyon, Marcus, Yvonne, Lu, Chunrong, Mash, Deborah C., Volpi, Simona, Struewing, Jeff, Colantuoni, Deborah, Little, Roger, Koester, Susan, Carithers, NCI Latarsha J., Moore, Helen M., Guan, Ping, Sawyer, Sherilyn J., Demchok, Joanne P., Vaught, Jimmie B., Rabiner, Chana A.
Published in Scientific reports

Secondary Precursor T-Cell Lymphoblastic Lymphoma Following Precursor B-cell Acute Lymphoblastic Leukemia: A Case Report and Review of the Literature

by Jenny L. Smith, Albert Kheradpour, Craig W. Zuppan, Jun Wang, Rhett P. Ketterling, Edward H. Rowsell
Published in Journal of cancer research updates

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...

by Göker, Erdem, Waltham, Mark, Kheradpour, Albert, Trippett, Tanya, Mazumdar, Madhu, Elisseyeff, Yaroslav, Schnieders, Barbara, Steinherz, Peter, Tan, Charlotte, Berman, Ellin, Bertino, Joseph R.
Published in Blood

Outcomes of Measurable Residual Disease in Pediatric Acute Myeloid Leukemia before and after Hematopoietic Stem Cell Transplant: Validation of Difference from Normal Flow Cytometry...

by 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.
Published in Biology of blood and marrow transplantation

A Comprehensive Map of Insulator Elements for the Drosophila Genome: e1000814

by Nègre, Nicolas, Brown, Christopher D, Shah, Parantu K, Kheradpour, Pouya, Morrison, Carolyn A, Henikoff, Jorja G, Feng, Xin, Ahmad, Kami, Russell, Steven, White, Robert AH, Stein, Lincoln, Henikoff, Steven, Kellis, Manolis, White, Kevin P
Published in PLoS genetics

Genome analysis of the platypus reveals unique signatures of evolution

by Warren, Wesley C, Hillier, LaDeana W, Marshall Graves, Jennifer A, Birney, Ewan, Ponting, Chris P, Grützner, Frank, Belov, Katherine, Miller, Webb, Clarke, Laura, Chinwalla, Asif T, Yang, Shiaw-Pyng, Heger, Andreas, Locke, Devin P, Miethke, Pat, Waters, Paul D, Veyrunes, Frédéric, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Wallis, John, Puente, Xose S, López-Otín, Carlos, Ordóñez, Gonzalo R, Eichler, Evan E, Chen, Lin, Cheng, Ze, Deakin, Janine E, Alsop, Amber, Thompson, Katherine, Kirby, Patrick, Papenfuss, Anthony T, Wakefield, Matthew J, Olender, Tsviya, Lancet, Doron, Huttley, Gavin A, Smit, Arian F. A, Pask, Andrew, Batzer, Mark A, Walker, Jerilyn A, Konkel, Miriam K, Harris, Robert S, Whittington, Camilla M, Wong, Emily S. W, Buschiazzo, Emmanuel, Vargas Jentzsch, Iris M, Merkel, Angelika, Schmitz, Juergen, Zemann, Anja, Churakov, Gennady, Kriegs, Jan Ole, Brosius, Juergen, Murchison, Elizabeth P, Sachidanandam, Ravi, Smith, Carly, Hannon, Gregory J, Tsend-Ayush, Enkhjargal, Attenborough, Rosalind, Rens, Willem, Ferguson-Smith, Malcolm, Lefèvre, Christophe M, Sharp, Julie A, Nicholas, Kevin R, Ray, David A, Kube, Michael, Reinhardt, Richard, Pringle, Thomas H, Taylor, James, Jones, Russell C, Nixon, Brett, Dacheux, Jean-Louis, Niwa, Hitoshi, Sekita, Yoko, Huang, Xiaoqiu, Stark, Alexander, Kheradpour, Pouya, Kellis, Manolis, Flicek, Paul, Chen, Yuan, Webber, Caleb, Hardison, Ross, Nelson, Joanne, Hallsworth-Pepin, Kym, Delehaunty, Kim, Markovic, Chris, Minx, Pat, Feng, Yucheng, Kremitzki, Colin, Glasscock, Jarret, Wylie, Todd, Wohldmann, Patricia, Thiru, Prathapan, Nhan, Michael N, Pohl, Craig S, Smith, Scott M, Hou, Shunfeng, Nefedov, Mikhail, de Jong, Pieter J, Renfree, Marilyn B, Mardis, Elaine R, Wilson, Richard K
Published in Nature (London)

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

by Rivas, Manuel A, Pirinen, Matti, Conrad, Donald F, Lek, Monkol, Tsang, Emily K, Karczewski, Konrad J, Maller, Julian B, Kukurba, Kimberly R, DeLuca, David S, Fromer, Menachem, Ferreira, Pedro G, Smith, Kevin S, Zhang, Rui, Zhao, Fengmei, Banks, Eric, Poplin, Ryan, Ruderfer, Douglas M, Purcell, Shaun M, Tukiainen, Taru, Minikel, Eric V, Stenson, Peter D, Cooper, David N, Huang, Katharine H, Sullivan, Timothy J, Nedzel, Jared, Bustamante, Carlos D, Li, Jin Billy, Daly, Mark J, Guigo, Roderic, Donnelly, Peter, Ardlie, Kristin, Sammeth, Michael, Dermitzakis, Emmanouil T, McCarthy, Mark I, Montgomery, Stephen B, Lappalainen, Tuuli, MacArthur, Daniel G
Published in Science (American Association for the Advancement of Science)