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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.
Cell Syst. 2019 Jul 24;9(1):24-34.e10. doi: 10.1016/j.cels.2019.06.006.
Cell Syst. 2019.
PMID: 31344359
Free PMC article.
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.
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Analytical protocol to identify local ancestry-associated molecular features in cancer.
Carrot-Zhang J, Han S, Zhou W, Damrauer JS, Kemal A; Cancer Genome Atlas Analysis Network; Cherniack AD, Beroukhim R.
Carrot-Zhang J, et al.
STAR Protoc. 2021 Sep 20;2(4):100766. doi: 10.1016/j.xpro.2021.100766. eCollection 2021 Dec 17.
STAR Protoc. 2021.
PMID: 34585150
Free PMC article.
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Analysis of germline-driven ancestry-associated gene expression in cancers.
Chambwe N, Sayaman RW, Hu D, Huntsman S; Cancer Genome Analysis Network; Kemal A, Caesar-Johnson S, Zenklusen JC, Ziv E, Beroukhim R, Cherniack AD.
Chambwe N, et al.
STAR Protoc. 2022 Jul 31;3(3):101586. doi: 10.1016/j.xpro.2022.101586. eCollection 2022 Sep 16.
STAR Protoc. 2022.
PMID: 35942349
Free PMC article.
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Ancestry-specific predisposing germline variants in cancer.
Oak N, Cherniack AD, Mashl RJ; TCGA Analysis Network; Hirsch FR, Ding L, Beroukhim R, Gümüş ZH, Plon SE, Huang KL.
Oak N, et al.
Genome Med. 2020 May 29;12(1):51. doi: 10.1186/s13073-020-00744-3.
Genome Med. 2020.
PMID: 32471518
Free PMC article.
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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.
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