Publications

Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C. Melms, Sebastian Niezen, Toni M. Delorey, Adam L. Essene, Olga R. Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S. Andrews, Carly G.K. Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M. Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J. Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F. Padera, Jr., Sonya A. MacParland, Gary D. Bader, Nasser Imad, Isaac H. Solomon, Eric Miller, Stefan Riedel, Caroline B.M. Porter, Alexandra-Chloé Villani, Linus T.-Y. Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K. Shalek, Benjamin Izar, Aviv Regev, Yury Popov, Z. Gordon Jiang, and Ioannis S. Vlachos.

Genome Biology 26(56), (2025).

BioRxiv Preprint, Posted October 28, 2022.

Collaboration with Regev Lab

Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen J. Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way.

Alessandro Arduini†, Stephen J. Fleming†, Ling Xiao†, Amelia W. Hall, Amer-Denis Akkad, Mark D. Chaffin, Kayla J. Bendinelli, Nathan R. Tucker, Irinna Papangeli, Helene Mantineo, Patricio Flores-Bringas, Mehrtash Babadi, Christian M. Stegmann, Guillermo García-Cardeña, Mark E. Lindsay, Carla Klattenhoff, and Patrick T. Ellinor (†: These authors contributed equally).

Cell Reports 44(1):115091, (2025).

BioRxiv Preprint, Posted November 16, 2023.

Collaboration with Ellinor Lab

ResearchSquare Preprint, posted July 8, 2024

Brice Wang, Tianle Ma, Theresa Chen, Trinh Nguyen, Ethan Crouse, Stephen J. Fleming, Alison S. Walker, Vera Valakh, Ralda Nehme, Evan W. Miller, Samouil L. Farhi, & Mehrtash Babadi.

npg Imaging 2(51), (2024).

BioRxiv Preprint, Posted April 15, 2024.

Yang Xu, Stephen J. Fleming, Matthew Tegtmeyer, Steven A. McCarroll & Mehrtash Babadi.

Cell Systems 16(4):101245. April 16, 2025.

BioRxiv Preprint, Posted March 16, 2024.

Collaboration with McCarroll Lab

Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A. Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A. Cimini, Anne E. Carpenter, Shantanu Singh, and Juan C. Caicedo.

Nature Communications 15, 1594 (2024).

Collaboration with Carpenter-Singh and Caicedo Labs

Erica Normandin, Sergio Triana, Siddharth S. Raju, Tammy C.T. Lan, Kim Lagerborg, Melissa Rudy, Gordon C. Adams, Katherine C. DeRuff, James Logue, David Liu, Daniel Strebinger, Arya Rao, Katelyn S. Messer, Molly Sacks, Ricky D. Adams, Krisztina Janosko, Dylan Kotliar, Rickey Shah, Ian Crozier, John L. Rinn, Marta Mele, Anna N. Honko, Feng Zhang, Mehrtash Babadi, Jeremy Luban, Richard S. Bennett, Alex K. Shalek, Nikolaos Barkas, Aaron E. Lin, Lisa E. Hensley, Pardis C. Sabeti, and Katherine J. Siddle.

Cell Genomics 3, 100440 (2023).

Collaboration with Sabeti Lab

Mehrtash Babadi, Jack M. Fu, Samuel K. Lee, Andrey N. Smirnov, Laura D. Gauthier, Mark Walker, David I. Benjamin, Xuefang Zhao, Konrad J. Karczewski, Isaac Wong, Ryan L. Collins, Alba Sanchis-Juan, Harrison Brand, Eric Banks, and Michael E. Talkowski.

Nature Genetics 55, 1589–1597 (2023).

Collaboration with Talkowski Lab

Stephen Fleming and Mehrtash Babadi.

Nature Methods 20, 1285–1286 (2023).

Stephen J. Fleming, Mark D. Chaffin, Alessandro Arduini, Amer-Denis Akkad, Eric Banks, John C. Marioni, Anthony A. Philippakis, Patrick T. Ellinor, and Mehrtash Babadi.

Nature Methods 20, 1323–1335 (2023).

Carmen Diaz Verdugo, Stephen Fleming, Nicole Deflaux and Amy Unruh.

Blog post hosted at both Terra and Carpenter-Singh Lab. (Aug 2023)

Collaboration with Carpenter-Singh Lab

Nir Hacohen, Aziz Al’Khafaji, Paul Blainey, Mehrtash Babadi, Kiran V. Garimella, Jonathan T. Smith.

US Patent US20230235394A1 (Filed June 14, 2021; Published July 27, 2023).

Collaboration with Methods Development Lab (MDL)

Aziz M. Al’Khafaji†, Jonathan T. Smith†, Kiran V. Garimella†, Mehrtash Babadi†, Victoria Popic†, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, and Nir Hacohen (†: These authors contributed equally).

Nature Biotechnology, 1-5 (2023).

Collaboration with Methods Development Lab (MDL)

Alyssa Wilson and Mehrtash Babadi.

Cell Patterns 4(4), 100693 (2023).

Collaboration with Icahn School of Medicine at Mount Sinai

Erica Normandin, Melissa Rudy, Nikolaos Barkas, Stephen F. Schaffner, Zoe Levine, Robert F. Padera Jr, Mehrtash Babadi, Shibani S. Mukerji, Daniel J. Park, Bronwyn L. MacInnis, Katherine J. Siddle, Pardis C. Sabeti, and Isaac H. Solomon.

Nature Communications 14, 574 (2023).

Collaboration with Sabeti Lab

Jack M. Fu, F. Kyle Satterstrom, Minshi Peng, Harrison Brand, Ryan L. Collins, Shan Dong, Brie Wamsley, Lambertus Klei, Lily Wang, Stephanie P. Hao, Christine R. Stevens, Caroline Cusick, Mehrtash Babadi, Eric Banks, Brett Collins, Sheila Dodge, Stacey B. Gabriel, Laura Gauthier, Samuel K. Lee, Lindsay Liang, Alicia Ljungdahl, Behrang Mahjani, Laura Sloofman, Andrey N. Smirnov, Mafalda Barbosa, Catalina Betancur, Alfredo Brusco, Brian H. Y. Chung, Edwin H. Cook, Michael L. Cuccaro, Enrico Domenici, Giovanni Battista Ferrero, J. Jay Gargus, Gail E. Herman, Irva Hertz-Picciotto, Patricia Maciel, Dara S. Manoach, Maria Rita Passos-Bueno, Antonio M. Persico, Alessandra Renieri, James S. Sutcliffe, Flora Tassone, Elisabetta Trabetti, Gabriele Campos, Simona Cardaropoli, Diana Carli, Marcus C. Y. Chan, Chiara Fallerini, Elisa Giorgio, Ana Cristina Girardi, Emily Hansen-Kiss, So Lun Lee, Carla Lintas, Yunin Ludena, Rachel Nguyen, Lisa Pavinato, Margaret Pericak-Vance, Isaac N. Pessah, Rebecca J. Schmidt, Moyra Smith, Claudia I. S. Costa, Slavica Trajkova, Jaqueline Y. T. Wang, Mullin H. C. Yu, The Autism Sequencing Consortium (ASC), Broad Institute Center for Common Disease Genomics (Broad-CCDG), iPSYCH-BROAD Consortium, David J. Cutler, Silvia De Rubeis, Joseph D. Buxbaum, Mark J. Daly, Bernie Devlin, Kathryn Roeder, Stephan J. Sanders, and Michael E. Talkowski.

Nature Genetics 54, 1320–1331 (2022).

Collaboration with Talkowski Lab

Mark Chaffin, Irinna Papangeli, Bridget Simonson, Amer-Denis Akkad, Matthew C. Hill, Alessandro Arduini, Stephen J. Fleming, Michelle Melanson, Sikander Hayat, Maria Kost-Alimova, Ondine Atwa, Jiangchuan Ye, Kenneth C. Bedi Jr, Matthias Nahrendorf, Virendar K. Kaushik, Christian M. Stegmann, Kenneth B. Margulies, Nathan R. Tucker & Patrick T. Ellinor.

Nature 608, 174–180 (2022)

Collaboration with Ellinor Lab

Fritz Obermeyer, Martin Jankowiak, Nikolaos Barkas, Stephen F. Schaffner, Jesse D. Pyle, Leonid Yurkovetskiy, Matteo Bosso, Daniel J. Park, Mehrtash Babadi, Bronwyn L. MacInnis, Jeremy Luban, Pardis C. Sabeti, and Jacob E. Lemieux.

Science 376, 1327–1332 (2022).

Collaboration with Sabeti Lab

Mehrtash Babadi, Luca D’Alessio, Muriel Medard, Ken Duffy, Yonina Eldar.

US Patent US20220358672A1 (2022).

James P. Pirruccello, Mark D. Chaffin, Elizabeth L. Chou, Stephen J. Fleming, Honghuang Lin, Mahan Nekoui, Shaan Khurshid, Samuel F. Friedman, Alexander G. Bick, Alessandro Arduini, Lu-Chen Weng, Seung Hoan Choi, Amer-Denis Akkad, Puneet Batra, Nathan R. Tucker, Amelia W. Hall, Carolina Roselli, Emelia J. Benjamin, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Christian M. Stegmann, Dejan Juric, James R. Stone, Ramachandran S. Vasan, Jennifer E. Ho, Udo Hoffmann, Steven A. Lubitz, Anthony A. Philippakis, Mark E. Lindsay & Patrick T. Ellinor.

Nature Genetics 54, 40–51 (2022)

Collaboration with Ellinor Lab

Toni M. Delorey, Carly G. K. Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Stephen J. Fleming, Ayshwarya Subramanian, Daniel T. Montoro, Karthik A. Jagadeesh, Kushal K. Dey, Pritha Sen, Michal Slyper, Yered H. Pita-Juárez, Devan Phillips, Jana Biermann, Zohar Bloom-Ackermann, Nikolaos Barkas, Andrea Ganna, James Gomez, Johannes C. Melms, Igor Katsyv, Erica Normandin, Pourya Naderi, Yury V. Popov, Siddharth S. Raju, Sebastian Niezen, Linus T.-Y. Tsai, Katherine J. Siddle, Malika Sud, Victoria M. Tran, Shamsudheen K. Vellarikkal, Yiping Wang, Liat Amir-Zilberstein, Deepak S. Atri, Joseph Beechem, Olga R. Brook, Jonathan Chen, Prajan Divakar, Phylicia Dorceus, Jesse M. Engreitz, Adam Essene, Donna M. Fitzgerald, Robin Fropf, Steven Gazal, Joshua Gould, John Grzyb, Tyler Harvey, Jonathan Hecht, Tyler Hether, Judit Jané-Valbuena, Michael Leney-Greene, Hui Ma, Cristin McCabe, Daniel E. McLoughlin, Eric M. Miller, Christoph Muus, Mari Niemi, Robert Padera, Liuliu Pan, Deepti Pant, Carmel Pe’er, Jenna Pfiffner-Borges, Christopher J. Pinto, Jacob Plaisted, Jason Reeves, Marty Ross, Melissa Rudy, Erroll H. Rueckert, Michelle Siciliano, Alexander Sturm, Ellen Todres, Avinash Waghray, Sarah Warren, Shuting Zhang, Daniel R. Zollinger, Lisa Cosimi, Rajat M. Gupta, Nir Hacohen, Hanina Hibshoosh, Winston Hide, Alkes L. Price, Jayaraj Rajagopal, Purushothama Rao Tata, Stefan Riedel, Gyongyi Szabo, Timothy L. Tickle, Patrick T. Ellinor, Deborah Hung, Pardis C. Sabeti, Richard Novak, Robert Rogers, Donald E. Ingber, Z. Gordon Jiang, Dejan Juric, Mehrtash Babadi, Samouil L. Farhi, Benjamin Izar, James R. Stone, Ioannis S. Vlachos, Isaac H. Solomon, Orr Ashenberg, Caroline B. M. Porter, Bo Li, Alex K. Shalek, Alexandra-Chloé Villani, Orit Rozenblatt-Rosen, and Aviv Regev.

Nature 595, 107–113 (2021).

Collaboration with Regev Lab

Luca D’Alessio, Litian Liu, Ken Duffy, Yonina C. Eldar, Muriel Médard, and Mehrtash Babadi.

IEEE, 2020 International Symposium on Information Theory and Its Applications (ISITA) (24-27 October 2020).

Nathan R. Tucker, Mark Chaffin, Stephen J. Fleming, Amelia W. Hall, Victoria A. Parsons, Kenneth C. Bedi Jr, Amer-Denis Akkad, Caroline N. Herndon, Alessandro Arduini, Irinna Papangeli, Carolina Roselli, François Aguet, Seung Hoan Choi, Kristin G. Ardlie, Mehrtash Babadi, Kenneth B. Margulies, Christian M. Stegmann and Patrick T. Ellinor.

Circulation 142(5), 466-482 (2020).

Collaboration with Ellinor Lab

Sachet A. Shukla, Pavan Bachireddy, Bastian Schilling, Christina Galonska, Qian Zhan, Clyde Bango, Rupert Langer, Patrick C. Lee, Daniel Gusenleitner, Derin B. Keskin, Mehrtash Babadi, Arman Mohammad, Andreas Gnirke, Kendell Clement, Zachary J. Cartun, Eliezer M. Van Allen, Diana Miao, Ying Huang, Alexandra Snyder, Taha Merghoub, Jedd D. Wolchok, Levi A. Garraway, Alexander Meissner, Jeffrey S. Weber, Nir Hacohen, Donna Neuberg, Patrick R. Potts, George F. Murphy, Christine G. Lian, Dirk Schadendorf, F. Stephen Hodi, and Catherine J. Wu.

Cell 173, 624–633 (2018).

Collaboration with Wu Lab