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.
BioRxiv Preprint, Posted April 15, 2024.
Publications
2024
Robust self-supervised denoising of voltage imaging data using CellMincer
Modeling interpretable correspondence between cell state and perturbation response with CellCap
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BioRxiv Preprint, Posted March 16, 2024.
Collaboration with McCarroll Lab
Learning representations for image-based profiling of perturbations
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
2023
Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
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
Reproducible image-based profiling with Pycytominer
Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen 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.
Collaboration with Carpenter-Singh Lab
Transcriptional profile of the rat cardiovascular system at single cell resolution
Alessandro Arduini†, Stephen J. Fleming†, Ling Xiao†, Amelia W Hall, Amer-Denis Akkad, Mark Chaffin, Kayla J Bendinelli, Nathan R Tucker, Irinna Papangeli, Helene Mantineo, Mehrtash Babadi, Christian M Stegmann, Guillermo García-Cardeña, Mark E Lindsay, Carla Klattenhoff, and Patrick T Ellinor (†: These authors contributed equally).
BioRxiv Preprint, Posted November 16, 2023.
Collaboration with Ellinor Lab
GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
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
CellBender removes technical artifacts from single-cell RNA sequencing data
Stephen Fleming and Mehrtash Babadi.
Nature Methods 20, 1285–1286 (2023).
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender
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).
Microscopy in the cloud: CellProfiler and Cell Painting on Terra
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
Chimeric amplicon array sequencing
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)
High-throughput RNA isoform sequencing using programmed cDNA concatenation
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)
SynapseCLR: Uncovering features of synapses in primary visual cortex through contrastive representation learning
Alyssa Wilson and Mehrtash Babadi.
Cell Patterns 4(4), 100693 (2023).
Collaboration with Icahn School of Medicine at Mount Sinai
2022
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
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.
BioRxiv Preprint, Posted October 28, 2022.
Collaboration with Regev Lab
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection
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
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
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
Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
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
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
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
Coding for multiplexed fluorescence microscopy
Mehrtash Babadi, Luca D’Alessio, Muriel Medard, Ken Duffy, Yonina Eldar.
US Patent US20220358672A1 (2022).
2021
Deep learning enables genetic analysis of the human thoracic aorta
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
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
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
A Coding Theory Perspective on Multiplexed Molecular Profiling of Biological Tissues
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).
2020
Transcriptional and Cellular Diversity of the Human Heart
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
2018
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade
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