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Page 1
The chromatin accessibility landscape of primary human cancers.
Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network; Greenleaf WJ, Chang HY. Corces MR, et al. Science. 2018 Oct 26;362(6413):eaav1898. doi: 10.1126/science.aav1898. Science. 2018. PMID: 30361341 Free PMC article.
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers.
Sundaram L, Kumar A, Zatzman M, Salcedo A, Ravindra N, Shams S, Louie BH, Bagdatli ST, Myers MA, Sarmashghi S, Choi HY, Choi WY, Yost KE, Zhao Y, Granja JM, Hinoue T, Hayes DN, Cherniack A, Felau I, Choudhry H, Zenklusen JC, Farh KK, McPherson A, Curtis C, Laird PW; Cancer Genome Atlas Analysis Network‡; Demchok JA, Yang L, Tarnuzzer R, Caesar-Johnson SJ, Wang Z, Doane AS, Khurana E, Castro MAA, Lazar AJ, Broom BM, Weinstein JN, Akbani R, Kumar SV, Raphael BJ, Wong CK, Stuart JM, Safavi R, Benz CC, Johnson BK, Kyi C, Shen H, Corces MR, Chang HY, Greenleaf WJ. Sundaram L, et al. Science. 2024 Sep 6;385(6713):eadk9217. doi: 10.1126/science.adk9217. Epub 2024 Sep 6. Science. 2024. PMID: 39236169
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer.
Carrot-Zhang J, Chambwe N, Damrauer JS, Knijnenburg TA, Robertson AG, Yau C, Zhou W, Berger AC, Huang KL, Newberg JY, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E; Cancer Genome Atlas Analysis Network; Cherniack AD, Beroukhim R. Carrot-Zhang J, et al. Cancer Cell. 2020 May 11;37(5):639-654.e6. doi: 10.1016/j.ccell.2020.04.012. Cancer Cell. 2020. PMID: 32396860 Free PMC article.
Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.
Ellrott K, Wong CK, Yau C, Castro MAA, Lee JA, Karlberg BJ, Grewal JK, Lagani V, Tercan B, Friedl V, Hinoue T, Uzunangelov V, Westlake L, Loinaz X, Felau I, Wang PI, Kemal A, Caesar-Johnson SJ, Shmulevich I, Lazar AJ, Tsamardinos I, Hoadley KA; Cancer Genome Atlas Analysis Network; Robertson AG, Knijnenburg TA, Benz CC, Stuart JM, Zenklusen JC, Cherniack AD, Laird PW. Ellrott K, et al. Cancer Cell. 2025 Feb 10;43(2):195-212.e11. doi: 10.1016/j.ccell.2024.12.002. Epub 2025 Jan 2. Cancer Cell. 2025. PMID: 39753139 Free PMC article.
Three-dimensional genome landscape of primary human cancers.
Yost KE, Zhao Y, Hung KL, Zhu K, Xu D, Corces MR, Shams S, Louie BH, Sarmashghi S, Sundaram L, Luebeck J, Clarke S, Doane AS, Granja JM, Choudhry H, Imieliński M, Cherniack AD, Khurana E, Bafna V, Felau I, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network; Greenleaf WJ, Chang HY. Yost KE, et al. Nat Genet. 2025 May;57(5):1189-1200. doi: 10.1038/s41588-025-02188-0. Epub 2025 May 12. Nat Genet. 2025. PMID: 40355593 Free PMC article.
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles.
Bhinder B, Friedl V, Sethuraman S, Risso D, Chiotti KE, Mashl RJ, Ellrott KP, Lee JA, Wong CK, Gyan K, Deshpande A, Imielinski M, Bareja R, Stuart J, Peto M, Hoadley KA, Lazar AJ, Cherniack AD, Zhu J, Cao S, Rubin M, Wang W, Bathe OF, Robine N, Ding L, Laird PW, Zhou W, Shen H, Thorsson V, Yeh JJ, Bailey MH, Zhou DC, Peng XL, Goldman M, Li Y, Korkut A, Sahni N, Hayes DN, Mensah MKA, Felau I, Kemal A, Caesar-Johnson S, Demchok JA, Yang L, Ferguson ML, Tarnuzzer R, Wang Z, Zenklusen JC; Cancer Genome Atlas Analysis Network; Spellman P, Elemento O. Bhinder B, et al. Sci Rep. 2025 Jul 4;15(1):23921. doi: 10.1038/s41598-025-09075-y. Sci Rep. 2025. PMID: 40615649 Free PMC article.
Protocol for obtaining cancer type and subtype predictions using subSCOPE.
Grewal JK, Robertson AG, Ellrott K, Wong CK, Lee JA, Yau C, Tercan B, Castro MAA, Benz CC; Cancer Genome Atlas Analysis Network; Zenklusen JC, Cherniack AD, Laird PW, Jones SJM. Grewal JK, et al. STAR Protoc. 2025 Jun 20;6(2):103705. doi: 10.1016/j.xpro.2025.103705. Epub 2025 Apr 10. STAR Protoc. 2025. PMID: 40202838 Free PMC article.
Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods.
Tercan B, Apolonio VH, Chagas VS, Wong CK, Lee JA, Yau C, Benz CC, Stuart JM, Karlberg BJ, Ellrott K, Grewal JK, Jones SJM; Cancer Genome Atlas Analysis Network; Zenklusen JC, Robertson AG, Laird PW, Cherniack AD, Castro MAA. Tercan B, et al. STAR Protoc. 2025 Jun 20;6(2):103681. doi: 10.1016/j.xpro.2025.103681. Epub 2025 Mar 18. STAR Protoc. 2025. PMID: 40106435 Free PMC article.