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Cancer Program

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.

Dempster JM, Boyle I, Vazquez F, et al. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects. Genome Biol. 2021;22(1):343. doi:10.1186/s13059-021-02540-7

Analytical protocol to identify local ancestry-associated molecular features in cancer.

Carrot-Zhang J, Han S, Zhou W, et al. Analytical protocol to identify local ancestry-associated molecular features in cancer. STAR Protoc. 2021;2(4):100766. doi:10.1016/j.xpro.2021.100766

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

Raghavan S, Winter PS, Navia AW, et al. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell. 2021;184(25):6119-6137.e26. doi:10.1016/j.cell.2021.11.017

Age-related Diseases of Inflammation in Myelodysplastic Syndrome and Chronic Myelomonocytic Leukemia.

Weeks LD, Marinac CR, Redd RA, et al. Age-related Diseases of Inflammation in Myelodysplastic Syndrome and Chronic Myelomonocytic Leukemia. Blood. 2021. doi:10.1182/blood.2021014418

Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers.

Ito T, Young MJ, Li R, et al. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nat Genet. 2021;53(12):1664-1672. doi:10.1038/s41588-021-00967-z

Are CRISPR Screens Providing the Next Generation of Therapeutic Targets?

Vazquez F, Sellers WR. Are CRISPR Screens Providing the Next Generation of Therapeutic Targets? Cancer Res. 2021;81(23):5806-5809. doi:10.1158/0008-5472.CAN-21-1784

Racial, Ethnic, and Socioeconomic Disparities in Curative Treatment Receipt and Survival in Hepatocellular Carcinoma.

Wagle NS, Park S, Washburn D, et al. Racial, Ethnic, and Socioeconomic Disparities in Curative Treatment Receipt and Survival in Hepatocellular Carcinoma. Hepatol Commun. 2021. doi:10.1002/hep4.1863

Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer.

Coates JT, Sun S, Leshchiner I, et al. Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer. Cancer Discov. 2021;11(10):2436-2445. doi:10.1158/2159-8290.CD-21-0702

Biologically informed deep neural network for prostate cancer discovery.

Elmarakeby HA, Hwang J, Arafeh R, et al. Biologically informed deep neural network for prostate cancer discovery. Nature. 2021;598(7880):348-352. doi:10.1038/s41586-021-03922-4

Duplex-Repair enables highly accurate sequencing, despite DNA damage.

Xiong K, Shea D, Rhoades J, et al. Duplex-Repair enables highly accurate sequencing, despite DNA damage. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab855