Publications

Functional dissection of complex trait variants at single-nucleotide resolution

Nature 2026
Layla Siraj, Rodrigo I. Castro, Hannah B. Dewey, Susan Kales, John C. Butts, Thanh Thanh L. Nguyen, Masahiro Kanai, Daniel Berenzy, Kousuke Mouri, Qingbo S. Wang, Petko P. Fiziev, Kristin Tsuo, Zachary R. McCaw, Sager J. Gosai, François Aguet, Ran Cui, Irfahan Kassam, Jeremy McRae, Christopher M. Vockley, Caleb A. Lareau, Sergey Abramov, Alexandr Boystov, Jeff Vierstra, Yukinori Okada, Alexander Gusev, Thouis R. Jones, Eric S. Lander, Pardis C. Sabeti, Hilary K. Finucane, Steven K. Reilly, Jacob C. Ulirsch & Ryan Tewhey

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Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

BioRxiv 2025
John C. Butts, Stephen Rong, Sager J. Gosai, Rodrigo I. Castro, Mackenzie Noon, Kehinde Adeniran, Rohit Ghosh, Pardis C. Sabeti, Ryan Tewhey, Steven K. Reilly

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Integrating machine learning and functional genomics to study cross-species gene regulatory evolution

Current Opinion in Genetics & Development 2026
Erin N Gilbertson, Steven K. Reilly

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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

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Machine-guided design of cell-type-targeting 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

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Massively parallel approaches for characterizing noncoding functional variation in human evolution Author links open overlay panel

Current Opinion in Genetics & Development 2024
Stephen Rong, Elise Root, Steven K. Reilly

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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

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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

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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

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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

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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

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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

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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

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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)

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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)

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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

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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

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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

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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

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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

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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

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Evolution of gene regulation in humans

Annual Reviews 2016
Steven K Reilly, James P Noonan

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Origin and evolution of developmental enhancers in the mammalian neocortex

PNAS 2016
Deena Emera, Jun Yin, Steven K Reilly, Jake Gockley, James P Noonan

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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

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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

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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

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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

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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

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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

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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

Publications

Functional dissection of complex trait variants at single-nucleotide resolution

Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

Integrating machine learning and functional genomics to study cross-species gene regulatory evolution

Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes

Machine-guided design of cell-type-targeting cis-regulatory elements

Massively parallel approaches for characterizing noncoding functional variation in human evolution Author links open overlay panel

Multicenter integrated analysis of noncoding CRISPRi screens

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

The functional and evolutionary impacts of human-specific deletions in conserved elements

Evolutionary constraint and innovation across hundreds of placental mammals

Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells

Insights from complex trait fine-mapping across diverse populations

Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows

Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolution

Massively parallel discovery of human-specific substitutions that alter enhancer activity

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH

Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay

Evolution of gene regulation in humans

Origin and evolution of developmental enhancers in the mammalian neocortex

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

Evolutionary changes in promoter and enhancer activity during human corticogenesis

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism

The genomic landscape of cohesin-associated chromatin interactions

The evolution of lineage-specific regulatory activities in the human embryonic limb

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

Press

Research

Team