The Shah lab focuses on the major questions of cancer evolution: Why do some patients respond to treatment, while others succumb to the disease? Why do some treatments lose effectiveness over time? How do cancer cells acquire the ability to spread throughout the body? Using single cell genomics and transcriptomics, cellular imaging and state of the art machine learning tools we study the dynamics of cancer cells in patients before, during and after treatment.
Tracking clonal evolution during treatment in ovarian cancer using cell-free DNA.
Williams MJ, Vázquez-García I, Tam G, Wu M, Varice N, Havasov E, Shi H, Al-Rawi DH, Satas G, Lees HJ, Lee JJ, Myers MA, Zatzman M, Rusk N, Ali E, Shah RH, Berger MF, Mohibullah N, Lakhman Y, Chi DS, Abu-Rustum NR, Aghajanian C, McPherson A, Zamarin D, Loomis B, Weigelt B, Friedman CF, Shah SP*. Nature. 2025 Oct 1. doi: 10.1038/s41586-025-09580-0. Epub ahead of print. PMID: 41034582.
Ongoing genome doubling shapes evolvability and immunity in ovarian cancer.
McPherson A, Vázquez-García I, Myers MA, Al-Rawi DH, Zatzman M, Weiner AC, Freeman S, Mohibullah N, Satas G, Williams MJ, Ceglia N, Norkūnaitė D, Zhang AW, Li J, Lim JLP, Wu M, Choi S, Havasov E, Grewal D, Shi H, Kim M, Schwarz RF, Kaufmann T, Dinh KN, Uhlitz F, Tran J, Wu Y, Patel R, Ramakrishnan S, Kim D, Clarke J, Green H, Ali E, DiBona M, Varice N, Kundra R, Broach V, Gardner GJ, Roche KL, Sonoda Y, Zivanovic O, Kim SH, Grisham RN, Liu YL, Viale A, Rusk N, Lakhman Y, Ellenson LH, Tavaré S, Aparicio S, Chi DS, Aghajanian C, Abu-Rustum NR, Friedman CF, Zamarin D, Weigelt B, Bakhoum SF, Shah SP*. Nature. 2025 Aug;644(8078):1078-1087. doi: 10.1038/s41586-025-09240-3. Epub 2025 Jul 16. PMID: 40670783; PMCID: PMC12390843
Multimodal histopathologic models stratify hormone receptor-positive early breast cancer.
Boehm KM, El Nahhas OSM, Marra A, Waters M, Jee J, Braunstein L, Schultz N, Selenica P, Wen HY, Weigelt B, Paul ED, Cekan P, Erber R, Loeffler CML, Guerini-Rocco E, Fusco N, Frascarelli C, Mane E, Munzone E, Dellapasqua S, Zagami P, Curigliano G, Razavi P, Reis-Filho JS, Pareja F, Chandarlapaty S, Shah SP*, Kather JN. Nat Commun. 2025 Mar 2;16(1):2106. doi: 10.1038/s41467-025-57283-x. PMID: 40025017; PMCID: PMC11873197
Ovarian cancer mutational processes drive site-specific immune evasion.
Vázquez-García I, Uhlitz F, Ceglia N, Lim JLP, Wu M, Mohibullah N, Niyazov J, Ruiz AEB, Boehm KM, Bojilova V, Fong CJ, Funnell T, Grewal D, Havasov E, Leung S, Pasha A, Patel DM, Pourmaleki M, Rusk N, Shi H, Vanguri R, Williams MJ, Zhang AW, Broach V, Chi DS, Da Cruz Paula A, Gardner GJ, Kim SH, Lennon M, Long Roche K, Sonoda Y, Zivanovic O, Kundra R, Viale A, Derakhshan FN, Geneslaw L, Issa Bhaloo S, Maroldi A, Nunez R, Pareja F, Stylianou A, Vahdatinia M, Bykov Y, Grisham RN, Liu YL, Lakhman Y, Nikolovski I, Kelly D, Gao J, Schietinger A, Hollmann TJ, Bakhoum SF, Soslow RA, Ellenson LH, Abu-Rustum NR, Aghajanian C, Friedman CF, McPherson A, Weigelt B, Zamarin D, Shah SP. Nature. 2022 Dec;612(7941):778-786.. Epub 2022 Dec 14. PMID: 36517593; PMCID: PMC9771812.
Single-cell genomic variation induced by mutational processes in cancer.
Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN; IMAXT Consortium; Shah SP, Aparicio S. Nature. 2022 Dec;612(7938):106-115. Epub 2022 Oct 26. PMID: 36289342; PMCID: PMC9712114.
Vanguri RS, Luo J, Aukerman AT, Egger JV, Fong CJ, Horvat N, Pagano A, Araujo-Filho JAB, Geneslaw L, Rizvi H, Sosa R, Boehm KM, Yang SR, Bodd FM, Ventura K, Hollmann TJ, Ginsberg MS, Gao J; MSK MIND Consortium; Hellmann MD, Sauter JL, Shah SP. Nat Cancer. 2022 Oct;3(10):1151-1164.Epub 2022 Aug 29. PMID: 36038778; PMCID: PMC9586871.
Boehm KM, Aherne EA, Ellenson L, Nikolovski I, Alghamdi M, Vázquez-García I, Zamarin D, Long Roche K, Liu Y, Patel D, Aukerman A, Pasha A, Rose D, Selenica P, Causa Andrieu PI, Fong C, Capanu M, Reis-Filho JS, Vanguri R, Veeraraghavan H, Gangai N, Sosa R, Leung S, McPherson A, Gao J; MSK MIND Consortium; Lakhman Y, Shah SP. Nat Cancer. 2022 Jun;3(6):723-733. Epub 2022 Jun 28. PMID: 35764743; PMCID: PMC9239907.
Please visit Dr. Shah’s faculty page, PubMed or Google Scholar for more publications.
