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

by Kheradpour, Pouya, Kellis, Manolis
Published 2014

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

by Kheradpour, Pouya, Kellis, Manolis
Published 2013

Comparative analysis of regulatory information and circuits across distant species

by Kheradpour, Pouya, Kundaje, Anshul, Wu, Yi-Chieh, Kellis, Manolis
Published 2016

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

by Ward, Lucas D., Kheradpour, Pouya, Iriarte, Benjamin, Kellis, Manolis
Published 2016

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

by Ward, Lucas D., Kheradpour, Pouya, Iriarte, Benjamin, Kamvysselis, Manolis
Published 2019

A Cis-Regulatory Map of the Drosophila Genome

by Bristow, Christopher A., Kheradpour, Pouya, Sealfon, Rachel Sima, Kellis, Manolis
Published 2012

Evidence of reduced recombination rate in human regulatory domains

by Ernst, Jason, Liu, Yaping, Sarkar, Abhishek Kulshreshtha, Kheradpour, Pouya, Kellis, Manolis
Published 2017

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

by Lin, Michael F., Kheradpour, Pouya, Mag Washietl, Stefan, Parker, Brian J., Pedersen, Jakob S., Kellis, Manolis
Published 2012

A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals

by Mag Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Ward, Lucas D., Jungreis, Irwin, Rasmussen, Matthew D., Kellis, Manolis
Published 2012

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

by Kheradpour, Pouya, Kellis, Manolis, Ernst, Jason, Melnikov, Alexandre, Rogov, Peter, Wang, Li, Zhang, Xiaolan, Alston, Jessica, Mikkelsen, Tarjei Sigurd
Published 2013

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

by Spivakov, Mikhail, Akhtar, Junaid, Kheradpour, Pouya, Beal, Kathryn, Girardot, Charles, Koscielny, Gautier, Herrero, Javier, Kellis, Manolis, Furlong, Eileen E. M., Birney, Ewan
Published 2012

An integrated encyclopedia of DNA elements in the human genome

by Altshuler, Robert Charles, Ernst, Jason, Kellis, Manolis, Kheradpour, Pouya, Ward, Lucas D., Eaton, Matthew Lucas, Hendrix, David A., Jungreis, Irwin, Lin, Michael F., Washietl, Stefan
Published 2014

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

by 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
Published 2014

Mapping and Analysis of Chromatin State Dynamics in Nine Human Cell Types

by Ernst, Jason, Kheradpour, Pouya, Mikkelsen, Tarjei Sigurd, Shoresh, Noam, Ward, Lucas D., Epstein, Charles B., Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Ku, Manching, Durham, Timothy, Kellis, Manolis, Bernstein, Bradley E.
Published 2012

A Comprehensive Map of Insulator Elements for the Drosophila Genome

by White, Kevin P., Henikoff, Steven, Stein, Lincoln, White, Robert A. H., Russell, Steven, Ahmad, Kami, Feng, Xin, Henikoff, Jorja G., Morrison, Carolyn A., Shah, Parantu K., Brown, Christopher D., Negre, Nicolas, Kheradpour, Pouya, Kellis, Manolis
Published 2010

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

by Kheradpour, Pouya, Bristow, Christopher A., Mag Washietl, Stefan, Ay, Ferhat, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel Sima, Will, Sebastian, Berger, Bonnie, Kellis, Manolis, Roy, Sushmita, Ernst, Jason, Lin, Michael F., Meyer, Patrick E., Di Stefano, Luisa, Candeias, Rogerio, Nordman, Jared T., Orr-Weaver, Terry L.
Published 2013

The 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 2014

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

by Bernstein, Bradley E., Epstein, Charles B., Shoresh, Noam, Ernst, Jason, Mikkelsen, Tarjei Sigurd, Kheradpour, Pouya, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Ward, Lucas D., Altshuler, Robert Charles, Lin, Michael F., Kellis, Manolis, ENCODE Project Consortium
Published 2011

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, Negre, 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 2014