Publications

Machine-guided design of synthetic cell type-specific cis-regulatory elements

BioRxiv 2023

Sager J. Gosai#,+, Rodrigo I. Castro#,+, Natalia Fuentes, John C. Butts, Susan Kales, Ramil R. Noche, Kousuke Mouri, Pardis C. Sabeti^, Steven K. Reilly^,#, Ryan Tewhey^,#

+Contributed equally
^Jointly supervised this work
#Corresponding

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

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

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

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

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

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

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)

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)

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

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