@article{varma2026interpretable,title={Toward interpretable foundation models for molecular biology},author={Varma, Mukund and Ideker, Trey},journal={Molecular Cell},volume={86},number={20},pages={4097--4107},year={2026},publisher={Cell Press},doi={10.1016/j.molcel.2026.09.030},}
Cancer Res Commun
Development and validation of a multimodal–multitask deep learning approach for estimating late distant recurrence risk in HR-positive early breast cancer
Eleftherios P. Mamounas, Ming Chen, Joseph A. Sparano, and 23 more authors
@article{mamounas2026multimodal,title={Development and validation of a multimodal--multitask deep learning approach for estimating late distant recurrence risk in HR-positive early breast cancer},author={Mamounas, Eleftherios P. and Chen, Ming and Sparano, Joseph A. and Rahman, Md Ashequr and Cheng, Yating and Wang, Victoria and Gray, Robert J. and Rastogi, Priya and Amidi, Eghbal and Geyer, Charles E. and Boucher, Tommy and Freeman, Tanner J. and Ramzanpour, Mohammadreza and Varma, Mukund and Ghani, Hassan and Cheng, Caleb and Bales, Casey and Ribeiro, Jennifer R. and Bandos, Hanna and Stransky, Nicolas and Miglarese, Mark R. and Oberley, Matthew and Spetzler, David and Radovich, Milan and Sledge, George W. and Wolmark, Norman},journal={Cancer Research Communications},volume={6},number={7},pages={1825--1835},year={2026},publisher={American Association for Cancer Research},doi={10.1158/2767-9764.CRC-26-0362},}
bioRxiv
Single-cell trajectories in metastatic urothelial carcinoma reveal tumor–immune reprogramming and macrophage-driven resistance to PD-(L)1 blockade
Ronan Flippot, Amélie Roehrig, Julien Vibert, and 22 more authors
@article{flippot2026urothelial,preprint={true},title={Single-cell trajectories in metastatic urothelial carcinoma reveal tumor--immune reprogramming and macrophage-driven resistance to PD-(L)1 blockade},author={Flippot, Ronan and Roehrig, Am{\'e}lie and Vibert, Julien and Stransky, Nicolas and Cabel, Luc and Mulder, Kevin and Besse, Benjamin and Nicotra, Claudio and Ngo Camus, Maud and Massard, Christophe and Rouleau, Etienne and Jules-Clement, Gerome and Tran-Dien, Alicia and Tselikas, Lambros and Thibault, Constance and Bennamoun, Mostefa and Smolen, Gromoslaw A. and Varma, Mukund and Kulicke, Ruth and Scoazec, Jean-Yves and Vallot, C{\'e}line and Kamal, Maud and Peltier, Agathe and Letouz{\'e}, Eric and Loriot, Yohann},journal={bioRxiv},year={2026},doi={10.1101/2026.03.31.715549},}
@article{richards2025carisCombatseq,preprint={true},title={Caris-ComBat-seq: directionally harmonizing large-scale RNA-seq datasets},author={Richards, Laura M. and Varma, Mukund and Spies, Noah and Stransky, Nicolas and Davis, Fred P.},journal={bioRxiv},year={2025},doi={10.1101/2025.11.26.690779},}
npj Precis Oncol
Predicting ROS1 and ALK fusions in NSCLC from H&E slides with a two-step vision transformer approach
Eghbal Amidi, Mohammadreza Ramzanpour, Ming Chen, and 9 more authors
@article{amidi2025ros1alk,author={Amidi, Eghbal and Ramzanpour, Mohammadreza and Chen, Ming and Boucher, Tommy and Varma, Mukund and Samec, Timothy and Lamon, Brian and Stransky, Nicolas and Miglarese, Mark R. and Oberley, Matthew and Spetzler, David and Sledge, George W.},journal={npj Precision Oncology},volume={9},number={1},pages={266},year={2025},publisher={Nature Publishing Group},doi={10.1038/s41698-025-01037-x},}
2023
IBD
Single cell RNA sequencing of ulcerative colitis and Crohn’s disease tissue samples informs the selection of TREM1 as a target for the treatment of inflammatory bowel diseases
Sarah Grant, Kristen Johnson, Tom Thomas, and 14 more authors
@article{grant2023trem1,title={Single cell RNA sequencing of ulcerative colitis and Crohn's disease tissue samples informs the selection of TREM1 as a target for the treatment of inflammatory bowel diseases},author={Grant, Sarah and Johnson, Kristen and Thomas, Tom and Honig, Gerard and Bielecki, Piotr and Dendrou, Calliope and Guo, Sean and Kulicke, Ruth and Li, Ping and L'Italien, Larry and Spies, Noah and Stransky, Nicolas and Uhlig, Holm and Varma, Mukund and Travis, Simon and Buckley, Christopher and Magram, Jeanne},journal={Inflammatory Bowel Diseases},volume={29},number={Supplement\_1},pages={S52--S53},year={2023},publisher={Oxford University Press},doi={10.1093/ibd/izac247.102},}
2022
PLoS Biol
Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing
Guadalupe J. Jasso, Alok Jaiswal, Mukund Varma, and 11 more authors
@article{jasso2022colonstroma,title={Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing},author={Jasso, Guadalupe J. and Jaiswal, Alok and Varma, Mukund and Laszewski, Tyler and Grauel, Angelo and Omar, Abdifatah and Silva, Nilsa and Dranoff, Glenn and Porter, Jeffrey A. and Mansfield, Keith and Cremasco, Viviana and Regev, Aviv and Xavier, Ramnik J. and Graham, Daniel B.},journal={PLoS Biology},volume={20},number={1},pages={e3001532},year={2022},publisher={Public Library of Science},doi={10.1371/journal.pbio.3001532},}
2020
J Immunol
Cell type– and stimulation-dependent transcriptional programs regulated by Atg16L1 and its Crohn’s disease risk variant T300A
Mukund Varma, Motohiko Kadoki, Ariel Lefkovith, and 10 more authors
@article{varma2020atg16l1,title={Cell type-- and stimulation-dependent transcriptional programs regulated by Atg16L1 and its Crohn's disease risk variant T300A},author={Varma, Mukund and Kadoki, Motohiko and Lefkovith, Ariel and Conway, Kara L. and Gao, Kevin and Mohanan, Vishnu and Tusi, Betsabeh Khoramian and Graham, Daniel B. and Latorre, Isabel J. and Tolonen, Andrew C. and Khor, Bernard and Ng, Aylwin and Xavier, Ramnik J.},journal={The Journal of Immunology},volume={205},number={2},pages={414--424},year={2020},publisher={American Association of Immunologists},doi={10.4049/jimmunol.1900750},}
2018
Cell Host Microbe
Murine norovirus infection induces TH1 inflammatory responses to dietary antigens
Romain Bouziat, Scott B. Biering, Elaine Kouame, and 11 more authors
@article{bouziat2018norovirus,title={Murine norovirus infection induces TH1 inflammatory responses to dietary antigens},author={Bouziat, Romain and Biering, Scott B. and Kouame, Elaine and Sangani, Kishan A. and Kang, Soowon and Ernest, Jordan D. and Varma, Mukund and Brown, Judy J. and Urbanek, Kelly and Dermody, Terence S. and Ng, Aylwin and Hinterleitner, Reinhard and Hwang, Seungmin and Jabri, Bana},journal={Cell Host \& Microbe},volume={24},number={5},pages={677--688.e5},year={2018},publisher={Cell Press},doi={10.1016/j.chom.2018.10.004},}
Nat Med
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes
Daniel B. Graham, Chengwei Luo, Daniel J. O’Connell, and 10 more authors
@article{graham2018mhcii,title={Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes},author={Graham, Daniel B. and Luo, Chengwei and O'Connell, Daniel J. and Lefkovith, Ariel and Brown, Eric M. and Yassour, Moran and Varma, Mukund and Abelin, Jennifer G. and Conway, Kara L. and Jasso, Guadalupe J. and Matar, Caline G. and Carr, Steven A. and Xavier, Ramnik J.},journal={Nature Medicine},volume={24},number={11},pages={1762--1772},year={2018},publisher={Nature Publishing Group},doi={10.1038/s41591-018-0203-7},}
Cell Rep
Nitric oxide engages an anti-inflammatory feedback loop mediated by peroxiredoxin 5 in phagocytes
Daniel B. Graham, Guadalupe J. Jasso, Amanda Mok, and 9 more authors
@article{graham2018nitricoxide,title={Nitric oxide engages an anti-inflammatory feedback loop mediated by peroxiredoxin 5 in phagocytes},author={Graham, Daniel B. and Jasso, Guadalupe J. and Mok, Amanda and Goel, Gautam and Ng, Aylwin C. Y. and Kolde, Raivo and Varma, Mukund and Doench, John G. and Root, David E. and Clish, Clary B. and Carr, Steven A. and Xavier, Ramnik J.},journal={Cell Reports},volume={24},number={4},pages={838--850},year={2018},publisher={Cell Press},doi={10.1016/j.celrep.2018.06.081},}
2017
Science
Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease
Romain Bouziat, Reinhard Hinterleitner, Judy J. Brown, and 31 more authors
@article{bouziat2017reovirus,title={Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease},author={Bouziat, Romain and Hinterleitner, Reinhard and Brown, Judy J. and Stencel-Baerenwald, Jennifer E. and Ikizler, Mine and Mayassi, Toufic and Meisel, Marlies and Kim, Sangman M. and Discepolo, Valentina and Pruijssers, Andrea J. and Ernest, Jordan D. and Iskarpatyoti, Jason A. and Costes, L{\'e}a M. M. and Lawrence, Ian and Palanski, Brad A. and Varma, Mukund and Zurenski, Matthew A. and Khomandiak, Solomiia and McAllister, Nicole and Aravamudhan, Pavithra and Boehme, Karl W. and Hu, Fengling and Samsom, Janneke N. and Reinecker, Hans-Christian and Kupfer, Sonia S. and Guandalini, Stefano and Semrad, Carol E. and Abadie, Val{\'e}rie and Khosla, Chaitan and Barreiro, Luis B. and Xavier, Ramnik J. and Ng, Aylwin and Dermody, Terence S. and Jabri, Bana},journal={Science},volume={356},number={6333},pages={44--50},year={2017},publisher={American Association for the Advancement of Science},doi={10.1126/science.aah5298},}
2016
Cell Rep
TMEM258 is a component of the oligosaccharyltransferase complex controlling ER stress and intestinal inflammation
Daniel B. Graham, Ariel Lefkovith, Patrick Deelen, and 14 more authors
@article{graham2016tmem258,title={TMEM258 is a component of the oligosaccharyltransferase complex controlling ER stress and intestinal inflammation},author={Graham, Daniel B. and Lefkovith, Ariel and Deelen, Patrick and de Klein, Niek and Varma, Mukund and Boroughs, Angela and Desch, A. Nicole and Ng, Aylwin C. Y. and Guzman, Gaelen and Schenone, Monica and Petersen, Christine P. and Bhan, Atul K. and Rivas, Manuel A. and Daly, Mark J. and Carr, Steven A. and Wijmenga, Cisca and Xavier, Ramnik J.},journal={Cell Reports},volume={17},number={11},pages={2955--2965},year={2016},publisher={Cell Press},doi={10.1016/j.celrep.2016.11.042},}
Cell
Succinate dehydrogenase supports metabolic repurposing of mitochondria to drive inflammatory macrophages
Evanna L. Mills, Beth Kelly, Angela Logan, and 17 more authors
@article{mills2016sdh,author={Mills, Evanna L. and Kelly, Beth and Logan, Angela and Costa, Ana S. H. and Varma, Mukund and Bryant, Clare E. and Tourlomousis, Panagiotis and D{\"a}britz, J. Henry M. and Gottlieb, Eyal and Latorre, Isabel and Corr, Sin{\'e}ad C. and McManus, Gavin and Ryan, Dylan and Jacobs, Howard T. and Szibor, Marten and Xavier, Ramnik J. and Braun, Thomas and Frezza, Christian and Murphy, Michael P. and O'Neill, Luke A.},journal={Cell},volume={167},number={2},pages={457--470.e13},year={2016},publisher={Cell Press},doi={10.1016/j.cell.2016.08.064},}