Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

Por Kheradpour, Pouya, Kellis, Manolis
Publicado em 2014

Reliable prediction of regulator targets using 12 Drosophila genomes

Por Kheradpour, Pouya, Stark, Alexander, Roy, Sushmita, Kellis, Manolis
Publicado em 2007

Evidence of reduced recombination rate in human regulatory domains

Por Liu, Yaping, Sarkar, Abhishek, Kheradpour, Pouya, Ernst, Jason, Kellis, Manolis
Publicado no Genome Biol (2017)

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

Por Lin, Michael F., Kheradpour, Pouya, Washietl, Stefan, Parker, Brian J., Pedersen, Jakob S., Kellis, Manolis
Publicado em 2011

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Por Stark, Alexander, Kheradpour, Pouya, Parts, Leopold, Brennecke, Julius, Hodges, Emily, Hannon, Gregory J., Kellis, Manolis
Publicado em 2007

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

Por Kheradpour, Pouya, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei S., Kellis, Manolis
Publicado em 2013

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

Por Stark, Alexander, Bushati, Natascha, Jan, Calvin H., Kheradpour, Pouya, Hodges, Emily, Brennecke, Julius, Bartel, David P., Cohen, Stephen M., Kellis, Manolis
Publicado em 2008

Analysis of variation at transcription factor binding sites in Drosophila and humans

Por Spivakov, Mikhail, Akhtar, Junaid, Kheradpour, Pouya, Beal, Kathryn, Girardot, Charles, Koscielny, Gautier, Herrero, Javier, Kellis, Manolis, Furlong, Eileen EM, Birney, Ewan
Publicado em 2012

Conservation of small RNA pathways in platypus

Por Murchison, Elizabeth P., Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, Kellis, Manolis, Grützner, Frank, Stark, Alexander, Hannon, Gregory J.
Publicado em 2008

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

Por 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
Publicado em 2011

Systematic analysis of chromatin state dynamics in nine human cell types

Por 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.
Publicado em 2011

A Comprehensive Map of Insulator Elements for the Drosophila Genome

Por 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.
Publicado em 2010

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

Por 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., Marshall Graves, Jennifer A., Woods, Gregory M., Hannon, Gregory J., Papenfuss, Anthony T.
Publicado em 2010

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

Por 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.
Publicado em 2014

Histone Modifications at Human Enhancers Reflect Global Cell Type-Specific Gene Expression

Por 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, Jessica E., Liu, Hui, Zhang, Xinmin, Green, Roland D., Stewart, Ron, Thomson, James A., Crawford, Gregory E., Kellis, Manolis, Ren, Bing
Publicado em 2009

Comparative analysis of regulatory information and circuits across distant species

Por Boyle, Alan P., Araya, Carlos L., Brdlik, Cathleen, Cayting, Philip, Cheng, Chao, Cheng, Yong, Gardner, Kathryn, Hillier, LaDeana, 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
Publicado no Nature (2014)

A Cis-Regulatory Map of the Drosophila Genome

Por 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, Russell, Steven, Grossman, Robert L., Ren, Bing, Gerstein, Mark, Posakony, James W., Kellis, Manolis, White, Kevin P.
Publicado em 2011

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Por Stark, Alexander, Lin, Michael F., Kheradpour, Pouya, Pedersen, Jakob S., Parts, Leopold, Carlson, Joseph W., Crosby, Madeline A., Rasmussen, Matthew D., Roy, Sushmita, Deoras, Ameya N., Ruby, J. Graham, Brennecke, Julius, Hodges, Emily, Hinrichs, Angie S., Caspi, Anat, Paten, Benedict, Park, Seung-Won, Han, Mira V., Maeder, Morgan L., Polansky, Benjamin J., Robson, Bryanne E., Aerts, Stein, van Helden, Jacques, Hassan, Bassem, Gilbert, Donald G., Eastman, Deborah A., Rice, Michael, Weir, Michael, Hahn, Matthew W., Park, Yongkyu, Dewey, Colin N., Pachter, Lior, Kent, W. James, Haussler, David, Lai, Eric C., Bartel, David P., Hannon, Gregory J., Kaufman, Thomas C., Eisen, Michael B., Clark, Andrew G., Smith, Douglas, Celniker, Susan E., Gelbart, William M., Kellis, Manolis
Publicado em 2007

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

Por 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
Publicado em 2012

A high-resolution map of human evolutionary constraint using 29 mammals

Por Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B., Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R, Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis
Publicado em 2011