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Since July 2015, I have been a Scientist at Verily Life Sciences (formerly Google[x] Life Sciences). Prior to this, I earned my Ph.D. in Computer Science and continued as a postdoctoral associate in the Computational Biology Lab at MIT, led by Manolis Kellis. I earned a Bachelor and Master of Science in Computer Science from UIUC in Spring 2005. My research advisers were ChengXiang Zhai, Gene Robinson, and Charles Whitfield. My research interests include algorithms related to computational biology such as those dealing with regulatory element discovery using comparative genomics. More broadly, I am interested in algorithms, math and biology. In Fall 2008 I was a teaching assistant for an MIT computational biology course 6.047/6.878, which I also TAed in Fall 2005 when it was 6.095/6.895. In Spring 2004, Fall 2004 and Spring 2005 I was a TA for an introductory computer science course CS101 at UIUC. |
Publications
Early immune factors associated with the development of post-acute sequelae of SARS-CoV-2 infection in hospitalized and non-hospitalized individuals
Jacqueline M. Leung*, Michelle J. Wu*, Pouya Kheradpour*, Chen Chen, Katherine A. Drake, Gary Tong, Vanessa K. Ridaura, Howard C. Zisser, William A. Conrad, Natalia Hudson, Jared Allen, Christopher Welberry, Celine Parsy-Kowalska, Isabel Macdonald, Victor F. Tapson, James N. Moy, Christopher R. deFilippi, Ivan O. Rosas, Mujeeb Basit, Jerry A. Krishnan, Sairam Parthasarathy, Bellur S. Prabhakar, Mirella Salvatore, Charles C. Kim
Frontiers in Immunology, 2024 January 22, doi:10.3389/fimmu.2024.1348041
Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors
Katherine A. Drake*, Dimitri Talantov*, Gary J. Tong*, Jack T. Lin*, Simon Verheijden, Samuel Katz, Jacqueline M. Leung, Benjamin Yuen, Vinod Krishna, Michelle J. Wu, Alexander M. Sutherland, Sarah A. Short, Pouya Kheradpour, Maxwell R. Mumbach, Kate M. Franz, Vladimir Trifonov, Molly V. Lucas, James Merson, Charles C. Kim, The PRESCO Study Group
Clinical Immunology, 2023 October 16, doi:10.1016/j.clim.2023.109808
Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets
Michael H. Guo, Prashanth Sama, Brenna A. LaBarre, Hrishikesh Lokhande, John Balibalos, Ci Chu, Xiaomi Du, Pouya Kheradpour, Charles C. Kim, Taylor Oniskey, Thomas Snyder, Damien Z. Soghoian, Howard L. Weiner, Tanuja Chitnis, and Nikolaos A. Patsopoulos
Genome Biology, 2022 June 07, doi:10.1186/s13059-022-02694-y
Evidence of reduced recombination rate in human regulatory domains
Yaping Liu, Abhishek Sarkar, Pouya Kheradpour, Jason Ernst, and Manolis Kellis
Genome Biology, 2017 October 20, doi:10.1186/s13059-017-1308-x
The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
GTEx Consortium
Science, 2015 May 8, doi:10.1126/science.1262110
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Anshul Kundaje*, Wouter Meuleman*, Jason Ernst*, Misha Bilenky*, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, and Manolis Kellis
Nature, 2015 February 18, doi:10.1038/nature14248
Comparative analysis of regulatory information and circuits across distant species
Alan P. Boyle*, Carlos L. Araya*, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, and Michael Snyder
Nature, 2014 August 27, doi:10.1038/nature13668
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
Matthew Slattery*, Lijia Ma*, Rebecca F. Spokony*, Robert K. Arthur, Pouya Kheradpour, Anshul Kundaje, Nicolas Nègre, Alex Crofts, Ryan Ptashkin, Jennifer Zieba, Alexander Ostapenko, Sarah Suchy, Alec Victorsen, Nader Jameel, A. Jason Grundstad, Wenxuan Gao, Jennifer R. Moran, E. Jay Rehm, Robert L. Grossman, Manolis Kellis, and Kevin P. White
Genome Research, 2014 July 1, doi:10.1101/gr.168807.113
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
Pouya Kheradpour and Manolis Kellis
Nucleic Acids Research, 2013 December 13, doi:10.1093/nar/gkt1249
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
Pouya Kheradpour, Jason Ernst, Alexandre Melnikov, Peter Rogov, Li Wang, Xiaolan Zhang, Jessica Alston, Tarjei S. Mikkelsen, and Manolis Kellis
Genome Research, 2013 March 19, doi:10.1101/gr.144899.112
Analysis of variation at transcription factor binding sites in Drosophila and humans
Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, and Ewan Birney
Genome Biology, 2012 September 5, doi:10.1186/gb-2012-13-9-r49
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium
Nature, 2012 September 6, doi:10.1038/nature11247
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt*, Georgi K. Marinov*, Anshul Kundaje*, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, Peter Bickel, James B. Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles Epstein, Katherine I. Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J. Hartemink, Michael M. Hoffman, Vishwanath R. Iyer, Youngsook L. Jung, Subhradip Karmakar, Manolis Kellis, Peter V. Kharchenko, Qunhua Li, Tao Liu, X. Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, Richard M. Myers, Peter J. Park, Michael J. Pazin, Marc D. Perry, Debasish Raha, Timothy E. Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, John A. Stamatoyannopoulos, Michael Y. Tolstorukov, Kevin P. White, Simon Xi, Peggy J. Farnham, Jason D. Lieb, Barbara J. Wold, and Michael Snyder
Genome Research, 2012 September 5, doi:10.1101/gr.136184.111
Analysis of variation at transcription factor binding sites in Drosophila and humans
Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, and Ewan Birney
Genome Biology, 2012 September 5, doi:10.1186/gb-2012-13-9-r49
Computational Regulatory Genomics: Motifs, Networks, and Dynamics
Pouya Kheradpour
Ph.D. Thesis, MIT, 2012 February 3, doi:1721.1/70871
A high-resolution map of human evolutionary constraint using 29 mammals
Kerstin Lindblad-Toh, Manuel Garber*, Or Zuk*, Michael F. Lin*, Brian J. Parker*, Stefan Washietl*, Pouya Kheradpour*, Jason Ernst*, Gregory Jordan*, Evan Mauceli*, Lucas D. Ward*, Craig B. Lowe*, Alisha K. Holloway*, Michele Clamp*, Sante Gnerre*, Jessica Alföldi, Kathryn Beal, Jean Chang, Hiram Clawson, James Cuff, Federica Di Palma, Stephen Fitzgerald, Paul Flicek, Mitchell Guttman, Melissa J. Hubisz, David B. Jaffe, Irwin Jungreis, W. James Kent, Dennis Kostka, Marcia Lara, Andre L. Martins, Tim Massingham, Ida Moltke, Brian J. Raney, Matthew D. Rasmussen, Jim Robinson, Alexander Stark, Albert J. Vilella, Jiayu Wen, Xiaohui Xie, Michael C. Zody, Broad Institute Sequencing Platform Whole Genome Assembly Team, Kim C. Worley, Christie L. Kovar, Donna M. Muzny, Richard A. Gibbs, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Wesley C. Warren, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Genome Institute at Washington University, Ewan Birney, Elliott H. Margulies, Javier Herrero, Eric D. Green, David Haussler, Adam Siepel, Nick Goldman, Katherine S. Pollard, Jakob S. Pedersen, Eric S. Lander, and Manolis Kellis
Nature, 2011 October 27, doi:10.1038/nature10530
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
Michael F. Lin, Pouya Kheradpour, Stefan Washietl, Brian J. Parker, Jakob S. Pedersen, and Manolis Kellis
Genome Research, 2011 October 12, doi:10.1101/gr.108753.110
An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
Angeliki Magklara, Angela Yen*, Bradley M. Colquitt*, E. Josephine Clowney*, William Allen, Eirene Markenscoff-Papadimitriou, Zoe A. Evans, Pouya Kheradpour, George Mountoufaris, Catriona Carey, Gilad Barnea, Manolis Kellis, and Stavros Lomvardas
Cell, 2011 May 13, doi:10.1016/j.cell.2011.03.040
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
The ENCODE Project Consortium
PLoS Biology, 2011 April 19, doi:10.1371/journal.pbio.1001046
Mapping and analysis of chromatin state dynamics in nine human cell types
Jason Ernst, Pouya Kheradpour, Tarjei S. Mikkelsen, Noam Shoresh, Lucas D. Ward, Charles B. Epstein, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael Coyne, Manching Ku, Timothy Durham, Manolis Kellis*, and Bradley E. Bernstein*
Nature, 2011 May 5, doi:10.1038/nature09906
A cis-regulatory map of the Drosophila genome
Nicolas Nègre*, Christopher D. Brown*, Lijia Ma*, Christopher Aaron Bristow*, Steven W. Miller*, Ulrich Wagner*, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Mark Gerstein, Steven Russell, Robert L. Grossman, Bing Ren, James W. Posakony, Manolis Kellis, and Kevin P. White
Nature, 2011 March 24, doi:10.1038/nature09990
Identification of functional elements and regulatory circuits by Drosophila modENCODE
The modENCODE Consortium, Sushmita Roy*, Jason Ernst*, Peter V. Kharchenko*, Pouya Kheradpour*, Nicolas Nègre*, Matthew L. Eaton*, Jane M. Landolin*, Christopher A. Bristow*, Lijia Ma*, Michael F. Lin*, Stefan Washietl*, Bradley I. Arshinoff*, Ferhat Ay*, Patrick E. Meyer*, Nicolas Robine*, Nicole L. Washington*, Luisa Di Stefano*, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, and Manolis Kellis
Science, 2010 December 24, doi:10.1126/science.1198374
A comprehensive map of insulator elements for the Drosophila genome
Nicolas Nègre*, Christopher D. Brown*, Parantu K. Shah, Pouya Kheradpour, Carolyn A. Morrison, Jorja G. Henikoff, Xin Feng, Kami Ahmad, Steven Russell, Robert A. H. White, Lincoln Stein, Steven Henikoff, Manolis Kellis, and Kevin P. White
PLoS Genetics, 2010 January 15, doi:10.1371/journal.pgen.1000814
The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer
Elizabeth P. Murchison, Cesar Tovar, Arthur Hsu, Hannah S. Bender, Pouya Kheradpour, Clare A. Rebbeck, David Obendorf, Carly Conlan, Melanie Bahlo, Catherine A. Blizzard, Stephen Pyecroft, Alexandre Kreiss, Manolis Kellis, Alexander Stark, Timothy T. Harkins, Jennifer A. Marshall Graves, Gregory M. Woods, Gregory J. Hannon, and Anthony T. Papenfuss
Science, 2010 January 1, doi:10.1126/science.1180616
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Nathaniel D. Heintzman*, Gary C. Hon*, R. David Hawkins*, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, and Bing Ren
Nature, 2009 March 18, doi:10.1038/nature07829
Genome analysis of the platypus reveals unique signatures of evolution
Nature, 2008 May 8, doi:10.1038/nature06936
Conservation of small RNA pathways in platypus
Elizabeth P. Murchison, Pouya Kheradpour, Ravi Sachidanandam, Carly Smith, Emily Hodges, Zhenyu Xuan, Manolis Kellis, Frank Grützner, Alexander Stark, and Gregory J. Hannon
Genome Research, 2008 May 7, doi:10.1101/gr.073056.107
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands
Alexander Stark*, Natascha Bushati*, Calvin H. Jan, Pouya Kheradpour, Emily Hodges, Julius Brennecke, David P. Bartel, Stephen M. Cohen, and Manolis Kellis
Genes and Development, 2008 January 1, doi:10.1101/gad.1613108
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Alexander Stark*, Michael F. Lin*, Pouya Kheradpour*, Jakob S. Pedersen*, Leopold Parts, Joseph W. Carlson, Madeline A. Crosby, Matthew D. Rasmussen, Sushmita Roy, Ameya N. Deoras, J. Graham Ruby, Julius Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Emily Hodges, Angie S. Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V. Han, Morgan L. Maeder, Benjamin J. Polansky, Bryanne E. Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G. Gilbert, Deborah A. Eastman, Michael Rice, Michael Weir, Matthew W. Hahn, Yongkyu Park, Colin N. Dewey, Lior Pachter, W. James Kent, David Haussler, Eric C. Lai, David P. Bartel, Gregory J. Hannon, Thomas C. Kaufman, Michael B. Eisen, Andrew G. Clark, Douglas Smith, Susan E. Celniker, William M. Gelbart, and Manolis Kellis
Nature, 2007 November 8, doi:10.1038/nature06340
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium
Nature, 2007 November 8, doi:10.1038/nature06341
Reliable prediction of regulator targets using 12 Drosophila genomes
Pouya Kheradpour*, Alexander Stark*, Sushmita Roy, and Manolis Kellis
Genome Research, 2007 November 7, doi:10.1101/gr.7090407
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
Alexander Stark*, Pouya Kheradpour*, Leopold Parts, Julius Brennecke, Emily Hodges, Gregory J. Hannon, and Manolis Kellis
Genome Research, 2007 November 7, doi:10.1101/gr.6593807
Beyond the Bits: Cooperative Packet Recovery Using Physical Layer Information
Grace R. Woo, Pouya Kheradpour, Dawei Shen, and Dina Katabi
ACM MobiCom, 2007 September 9, doi:10.1145/1287853.1287871
Fold-specific substitution matrices for protein classification
Richard B. Vilim, R. M. Cunningham, Bo Lu, Pouya Kheradpour, and F. J. Stevens
Bioinformatics, 2004 February 5, doi:10.1093/bioinformatics/btg492
* indicates authors that contributed equally to the work.
Software
This is a collection of utilities I have written and released under the MIT License. Unless otherwise specified, see the file itself and/or run without arguments for usage details.
Heatmap.awk - produces highly customizable svg heatmaps
Plot.awk - produces scatter and bar plots
TT.awk - performs conversion, normalization, and other table operations
grep-overlap - computes overlaps between two sorted region files
Requires pk.h. Compile with: gcc -O3 -o grep-overlap grep-overlap.c
prec-overlap - flattens set of regions using precedence list
Requires pk.h. Compile with: gcc -O3 -o prec-overlap prec-overlap.c
motif-util - performs comparison, clustering, and other motif-related operations
Requires pk.h. Compile with: gcc -O3 -o motif-util motif-util.c -lm
motif-match - high speed matching of motifs to the genome or multiple alignments
extract-mfa - extract sequences from multiple alignments
apply-var - apply variants to output from extract-mfa
Requires pk.h. Compile with: gcc -O3 -o apply-var apply-var.c -lm
branch-sn - computes BLS to confidence mapping from motif instances
Please email me with any questions, including regarding citing this software, bug reports, or feature suggestions.