A supervised ontology-aware cell annotation method for single-cell transcriptomic data
Nimish Magre, Ebtisam Alshehri, Fedor Grab, Yerdos Ordabayev, Steven A. McCarroll, Mehrtash Babadi & Stephen J. Fleming. BioRxiv Preprint, Posted Jan 14, 2026.
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 […]
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
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. […]
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).
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, […]
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).
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 […]