Publications
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Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Science, 2024
Eduardo A. Maury, Attila Jones, Vladimir Seplyarskiy, Thanh Thanh L. Nguyen, Chaggai Rosenbluh, Taejong Bae, Yifan Wang, Alexej Abyzov, Sattar Khoshkhoo, Yasmine Chahine, Sijing Zhao, Sanan Venkatesh, Elise Root, Georgios Voloudakis, Panagiotis Roussos, Brain Somatic Mosaicism Network, Peter J. Park, Schahram Akbarian, Kristen Brennand, Steven Reilly, Eunjung A. Lee, Shamil R. Sunyaev, Christopher A. Walsh, Andrew Chess
Machine-guided design of synthetic cell type-specific cis-regulatory elements
Nature, 2024
Sager J. Gosai, Rodrigo I. Castro, Natalia Fuentes, John C. Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L. Nguyen, Ramil R. Noche, Arya S. Rao, Mary T. Joy, Pardis C. Sabeti, Steven K. Reilly & Ryan Tewhey
Massively parallel approaches for characterizing noncoding functional variation in human evolution
Current Opinion in Genetics & Development 2024
Stephen Rong, Elise Root, Steven K. Reilly
Functional dissection of complex and molecular trait variants at single nucleotide resolution
BioRxiv 2024
Layla Siraj, Rodrigo I. Castro, Hannah Dewey, Susan Kales, Thanh Thanh L. Nguyen, Masahiro Kanai, Daniel Berenzy, Kousuke Mouri, Qingbo S. Wang, Zachary R. McCaw, Sager J. Gosai, François Aguet, Ran Cui, Christopher M. Vockley, Caleb A. Lareau, Yukinori Okada, Alexander Gusev, Thouis R. Jones, Eric S. Lander, Pardis C. Sabeti, Hilary K. Finucane, Steven K. Reilly, Jacob C. Ulirsch, Ryan Tewhey
Multicenter integrated analysis of noncoding CRISPRi screens
Nature Methods 2024
David Yao, Josh Tycko, Jin Woo Oh, Lexi R. Bounds, Sager J. Gosai, Lazaros Lataniotis, Ava Mackay-Smith, Benjamin R. Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D. White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J. Greenleaf, Pardis C. Sabeti, Christina Leslie, Yuri Pritykin, Jill E. Moore, Michael A. Beer, Charles A. Gersbach, Timothy E. Reddy, Yin Shen, Jesse M. Engreitz, Michael C. Bassik, Steven K. Reilly
Evolutionary constraint and innovation across hundreds of placental mammals
Science 2023
Matthew J. Christmas, Irene M. Kaplow,†, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, Allyson G. Hindle, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Ana M. Breit, Mark Diekhans, Cornelia Fanter, Nicole M. Foley, Daniel B. Goodman, Linda Goodman, Kathleen C. Keough, Bogdan Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L. Lind, Jennifer R. S. Meadows, Lucas R. Moreira, Ruby W. Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R. Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna Grimshaw, Jeremy Johnson, Sergey V. Kozyrev, Alyssa J. Lawler, Voichita D. Marinescu, Kathleen M. Morrill, Austin Osmanski, Nicole S. Paulat, BaDoi N. Phan, Daniel E. Schäffer, Steven K. Reilly, Cynthia Steiner, Megan A. Supple, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Zoonomia Consortium, Bruce W. Birren, Steven Gazal, Robert M. Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K. Meyer, Martin Nweeia, Pardis C. Sabeti, Beth Shapiro, Arian F. A. Smit, Mark Springer, Emma Teeling, Zhiping Weng, Michael Hiller, Danielle L. Levesque, Harris A. Lewin, William J. Murphy, Arcadi Navarro, Benedict Paten, Katherine S. Pollard, David A. Ray, Irina Ruf, Oliver A. Ryder, Andreas R. Pfenning, Kerstin Lindblad-Toh, Elinor K. Karlsson
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Science 2021
Jacob E Lemieux, Katherine J Siddle, Bennett M Shaw, Christine Loreth, Stephen F Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H Tomkins-Tinch, Lydia A Krasilnikova, Katherine C DeRuff, Melissa Rudy, Matthew R Bauer, Kim A Lagerborg, Erica Normandin, Sinéad B Chapman, Steven K Reilly, Aaron E Lin, Amber Carter, Cameron Myhrvold, Molly E Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B Harris, John A Branda, David Hooper, Jessie M Gaeta, Travis P Baggett, James O’Connell, Andreas Gnirke, Tami D Lieberman, Anthony Philippakis, Meagan Burns, Catherine M Brown, Jeremy Luban, Edward T Ryan, Sarah E Turbett, Regina C LaRocque, William P Hanage, Glen R Gallagher, Lawrence C Madoff, Sandra Smole, Virginia M Pierce, Eric Rosenberg, Pardis C Sabeti, Daniel J Park, Bronwyn L MacInnis
Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Cell 2016
Ryan Tewhey, Dylan Kotliar, Daniel S Park, Brandon Liu, Sarah Winnicki, Steven K Reilly, Kristian G Andersen, Tarjei S Mikkelsen, Eric S Lander, Stephen F Schaffner, Pardis C Sabeti
Evolutionary changes in promoter and enhancer activity during human corticogenesis
Science 2015
Steven K Reilly, Jun Yin, Albert E Ayoub, Deena Emera, Jing Leng, Justin Cotney, Richard Sarro, Pasko Rakic, James P Noonan
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
Genome Research 2013
Justin Cotney, Jing Leng, Sunghee Oh, Laura E DeMare, Steven K Reilly, Mark B Gerstein, James P Noonan
Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows
Nature Microbiology 2022
Kim A Lagerborg, Erica Normandin, Matthew R Bauer, Gordon Adams, Katherine Figueroa, Christine Loreth, Adrianne Gladden-Young, Bennett Shaw, Leah Pearlman, Daniel Berenzy, Hannah B. Dewey, Susan Kales, Sabrina T. Dobbins, Erica S Shenoy, David Hooper, Virginia M Pierce, Kimon C Zachary, Daniel J Park, Bronwyn L MacInnis, Ryan Tewhey, Jacob E Lemieux, Pardis C Sabeti, Steven K Reilly*, Katherine J Siddle* (*denotes co-last)
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
Nature Genetics 2021
Steven K. Reilly, Sager J. Gosai, Alan Gutierrez, Ava Mackay-Smith, Jacob C. Ulirsch, Masahiro Kanai, Kousuke Mouri, Daniel Berenzy, Susan Kales, Gina M. Butler, Adrianne Gladden-Young, Redwan M. Bhuiyan, Michael L. Stitzel, Hilary K. Finucane, Pardis C. Sabeti & Ryan Tewhey
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
Cell 2013
A Jeremy Willsey, Stephan J Sanders, Mingfeng Li, Shan Dong, Andrew T Tebbenkamp, Rebecca A Muhle, Steven K Reilly, Leon Lin, Sofia Fertuzinhos, Jeremy A Miller, Michael T Murtha, Candace Bichsel, Wei Niu, Justin Cotney, A Gulhan Ercan-Sencicek, Jake Gockley, Abha R Gupta, Wenqi Han, Xin He, Ellen J Hoffman, Lambertus Klei, Jing Lei, Wenzhong Liu, Li Liu, Cong Lu, Xuming Xu, Ying Zhu, Shrikant M Mane, Ed S Lein, Liping Wei, James P Noonan, Kathryn Roeder, Bernie Devlin, Nenad Sestan, Matthew W State
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Cell 2022
Katherine J Siddle, Lydia A Krasilnikova, Gage K Moreno, Stephen F Schaffner, Johanna Vostok, Nicholas A Fitzgerald, Jacob E Lemieux, Nikolaos Barkas, Christine Loreth, Ivan Specht, Christopher H Tomkins-Tinch, Jillian S Paull, Beau Schaeffer, Bradford P Taylor, Bryn Loftness, Hillary Johnson, Petra L Schubert, Hanna M Shephard, Matthew Doucette, Timelia Fink, Andrew S Lang, Stephanie Baez, John Beauchamp, Scott Hennigan, Erika Buzby, Stephanie Ash, Jessica Brown, Selina Clancy, Seana Cofsky, Luc Gagne, Joshua Hall, Rachel Harrington, Gabrielle L Gionet, Katherine C DeRuff, Megan E Vodzak, Gordon C Adams, Sabrina T Dobbins, Sarah D Slack, Steven K Reilly, Lisa M Anderson, Michelle C Cipicchio, Matthew T DeFelice, Jonna L Grimsby, Scott E Anderson, Brendan S Blumenstiel, James C Meldrim, Heather M Rooke, Gina Vicente, Natasha L Smith, Katelyn S Messer, Faye L Reagan, Zoe M Mandese, Matthew D Lee, Marianne C Ray, Marissa E Fisher, Maesha A Ulcena, Corey M Nolet, Sean E English, Katie L Larkin, Kyle Vernest, Sushma Chaluvadi, Deirdre Arvidson, Maurice Melchiono, Theresa Covell, Vaira Harik, Taylor Brock-Fisher, Molly Dunn, Amanda Kearns, William P Hanage, Clare Bernard, Anthony Philippakis, Niall J Lennon, Stacey B Gabriel, Glen R Gallagher, Sandra Smole, Lawrence C Madoff, Catherine M Brown, Daniel J Park, Bronwyn L MacInnis, Pardis C Sabeti
Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution
Cell 2021
Dustin Griesemer*, James R Xue*, Steven K Reilly*, Jacob C Ulirsch, Kalki Kukreja, Joe Davis, Masahiro Kanai, David K Yang, John C. Butts, Mehmet H, Guney, Jermey Luban, Stephen B Montgomery, Carl D Novina, Hilary K. Finucane, Ryan Tewhey, Pardis C Sabeti (*denotes co-first)
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Nature Communications 2021
Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C. Ulirsch, Steven K Reilly, Duygu Ucar, Ryan Tewhey, Michael L Stitzel
Origin and evolution of developmental enhancers in the mammalian neocortex
PNAS 2016
Deena Emera, Jun Yin, Steven K Reilly, Jake Gockley, James P Noonan
The genomic landscape of cohesin-associated chromatin interactions
Genome Research 2013
Laura E DeMare, Jing Leng, Justin Cotney, Steven K Reilly, Jun Yin, Richard Sarro, James P Noonan
Leveraging base-pair mammalian constraint to understand genetic variation and human disease
Science 2023
Patrick F. Sullivan, Jennifer R. S. Meadows, Steven Gazal, BaDoi N. Phan, Xue Li, Diane P. Genereux, Michael X. Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J. Christmas, Voichita D. Marinescu, Chao Wang, Ola Wallerman, James Xue, Shuyang Yao, Quan Sun, Jin Szatkiewicz, Jia Wen, Laura M. Huckins, Alyssa Lawler, Kathleen C. Keough, Zhili Zheng, Jian Zeng, Naomi R. Wray, Yun Li, Jessica Johnson, Jiawen Chen, Zoonomia Consortium, Benedict Paten, Steven K. Reilly, Graham M. Hughes, Zhiping Weng, Katherine S. Pollard, Andreas R. Pfenning, Karin Forsberg-Nilsson, Elinor K. Karlsson, Kerstin Lindblad-Toh
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells
Molecular Biology and Evolution 2022
Evelyn Jagoda, James R Xue, Steven K Reilly, Michael Dannemann, Fernando Racimo, Emilia Huerta-Sanchez, Sriram Sankararaman, Janet Kelso, Luca Pagani, Pardis C Sabeti, Terence D Capellini
Massively parallel discovery of human-specific substitutions that alter enhancer activity
PNAS 2021
Severin Uebbing, Jake Gockley, Steven K Reilly, Acadia A Kocher, Evan Geller, Neeru Gandotra, Curt Scharfe, Justin Cotney, James P Noonan
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Nature Communications 2020
John P Ray, Carl G de Boer, Charles P Fulco, Caleb A Lareau, Masahiro Kanai, Jacob C Ulirsch, Ryan Tewhey, Leif S Ludwig, Steven K Reilly, Drew T Bergman, Jesse M Engreitz, Robbyn Issner, Hilary K Finucane, Eric S Lander, Aviv Regev, Nir Hacohen
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
Nature Communications 2015
Justin Cotney, Rebecca A Muhle, Stephan J Sanders, Li Liu, A Jeremy Willsey, Wei Niu, Wenzhong Liu, Lambertus Klei, Jing Lei, Jun Yin, Steven K Reilly, Andrew T Tebbenkamp, Candace Bichsel, Mihovil Pletikos, Nenad Sestan, Kathryn Roeder, Matthew W State, Bernie Devlin, James P Noonan
The evolution of lineage-specific regulatory activities in the human embryonic limb
Cell 2013
Justin Cotney, Jing Leng, Jun Yin, Steven K Reilly, Laura E DeMare, Deena Emera, Albert E Ayoub, Pasko Rakic, James P Noonan
The functional and evolutionary impacts of human-specific deletions in conserved elements
Science 2023
James R. Xue, Ava Mackay-Smith, Kousuke Mouri, Meilin Fernandez Garcia, Michael X. Dong, Jared F. Akers, Mark Noble, Xue Li, Zoonomia Consortium, Kerstin Lindblad-Toh, Elinor K. Karlsson, James P. Noonan, Terence D. Capellini, Kristen J. Brennand, Ryan Tewhey, Pardis C. Sabeti, Steven K. Reilly
Insights from complex trait fine-mapping across diverse populations
medRxiv
Masahiro Kanai, Jacob C Ulirsch, Juha Karjalainen, Mitja Kurki, Konrad J Karczewski, Eric Fauman, Qingbo S Wang, Hannah Jacobs, François Aguet, Kristin G Ardlie, Nurlan Kerimov, Kaur Alasoo, Christian Benner, Kazuyoshi Ishigaki, Saori Sakaue, Steven K Reilly, The BioBank Japan Project, FinnGen, Yoichiro Kamatani, Koichi Matsuda, Aarno Palotie, Benjamin M Neale, Ryan Tewhey, Pardis C Sabeti, Yukinori Okada, Mark J Daly, Hilary K Finucane
Press
NIH Director’s Blog on 2015 Science Paper
https://directorsblog.nih.gov/2015/03/17/what-makes-our-brain-human-the-search-for-answers/
Genome-wed article on human-specific brain development
https://www.genomeweb.com/epigenetics-research/study-links-regulatory-changes-during-development-human-cerebral-cortex
Reporting on advocacy work around LGBTQ GWAS
https://www.nytimes.com/2019/08/29/science/gay-gene-sex.html
https://www.wired.com/story/how-earnest-research-into-gay-genetics-went-wrong/
https://www.broadinstitute.org/blog/opinion-all-science-what-did-we-learn
Reporting on the development of DeepSweep
https://www.nature.com/articles/d41586-018-07225-z
For work on COVID-19 genome sequencing in Boston
https://www.nytimes.com/2020/08/26/health/covid-19-superspreaders-boston.html