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Epigenetic dysregulation from chromosomal transit in micronuclei.
Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Agustinus AS, et al. Among authors: shah sp. Nature. 2023 Jul;619(7968):176-183. doi: 10.1038/s41586-023-06084-7. Epub 2023 Jun 7. Nature. 2023. PMID: 37286593 Free PMC article.
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.
Zhang AW, O'Flanagan C, Chavez EA, Lim JLP, Ceglia N, McPherson A, Wiens M, Walters P, Chan T, Hewitson B, Lai D, Mottok A, Sarkozy C, Chong L, Aoki T, Wang X, Weng AP, McAlpine JN, Aparicio S, Steidl C, Campbell KR, Shah SP. Zhang AW, et al. Among authors: shah sp. Nat Methods. 2019 Oct;16(10):1007-1015. doi: 10.1038/s41592-019-0529-1. Epub 2019 Sep 9. Nat Methods. 2019. PMID: 31501550 Free PMC article.
Clonal fitness inferred from time-series modelling of single-cell cancer genomes.
Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA; IMAXT Consortium; McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Salehi S, et al. Among authors: shah sp. Nature. 2021 Jul;595(7868):585-590. doi: 10.1038/s41586-021-03648-3. Epub 2021 Jun 23. Nature. 2021. PMID: 34163070 Free PMC article.
Fundamental immune-oncogenicity trade-offs define driver mutation fitness.
Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Hoyos D, et al. Among authors: shah sp. Nature. 2022 Jun;606(7912):172-179. doi: 10.1038/s41586-022-04696-z. Epub 2022 May 11. Nature. 2022. PMID: 35545680 Free PMC article.
Author Correction: Fundamental immune-oncogenicity trade-offs define driver mutation fitness.
Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Hoyos D, et al. Among authors: shah sp. Nature. 2022 Jun;606(7914):E5. doi: 10.1038/s41586-022-04879-8. Nature. 2022. PMID: 35641605 Free PMC article. No abstract available.
Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer.
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. Boehm KM, et al. Among authors: shah sp. Nat Cancer. 2022 Jun;3(6):723-733. doi: 10.1038/s43018-022-00388-9. Epub 2022 Jun 28. Nat Cancer. 2022. PMID: 35764743 Free PMC article.
Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.
Martins FC, Couturier DL, de Santiago I, Sauer CM, Vias M, Angelova M, Sanders D, Piskorz A, Hall J, Hosking K, Amirthanayagam A, Cosulich S, Carnevalli L, Davies B, Watkins TBK, Funingana IG, Bolton H, Haldar K, Latimer J, Baldwin P, Crawford R, Eldridge M, Basu B, Jimenez-Linan M, Mcpherson AW, McGranahan N, Litchfield K, Shah SP, McNeish I, Caldas C, Evan G, Swanton C, Brenton JD. Martins FC, et al. Among authors: shah sp. Nat Commun. 2022 Oct 26;13(1):6360. doi: 10.1038/s41467-022-33870-0. Nat Commun. 2022. PMID: 36289203 Free PMC article.
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. Funnell T, et al. Among authors: shah sp. Nature. 2022 Dec;612(7938):106-115. doi: 10.1038/s41586-022-05249-0. Epub 2022 Oct 26. Nature. 2022. PMID: 36289342 Free PMC article.
391 results