McFarland, James M.

Next-generation characterization of the Cancer Cell Line Encyclopedia

Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., et al. (2019) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,394

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells

Meyers, R. M., Bryan, J. G., McFarland, J. M., Weir, B. A., Sizemore, A. E., Xu, H., Dharia, N. V., Montgomery, P. G., Cowley, G. S., Pantel, S., et al. (2017) · Nature Genetics

CRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Cited by 1,952

Discovering the anticancer potential of non-oncology drugs by systematic viability profiling

Corsello, S. M., Nagari, R. T., Spangler, R. D., Rossen, J., Kocak, M., Bryan, J. G., Humeidi, R., Peck, D., Wu, X., Tang, A. A., et al. (2020) · Nature Cancer

Computational Drug Discovery MethodsCancer Cells and Metastasis

Cited by 878

Patient-derived xenografts undergo mouse-specific tumor evolution

Ben-David, U., Ha, G., Tseng, Y.-Y., Greenwald, N. F., Oh, C., Shih, J., McFarland, J. M., Wong, B., Boehm, J. S., Beroukhim, R., et al. (2017) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 716

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

Raghavan, S., Winter, P. S., Navia, A. W., Williams, H. L., DenAdel, A., Lowder, K. E., Galvez-Reyes, J., Kalekar, R. L., Mulugeta, N., Kapner, K. S., et al. (2021) · Cell

Pancreatic and Hepatic Oncology ResearchSingle-cell and spatial transcriptomics

Cited by 592

Mutational processes shape the landscape of TP53 mutations in human cancer

Giacomelli, A. O., Yang, X., Lintner, R. E., McFarland, J. M., Duby, M., Kim, J., Howard, T. P., Takeda, D. Y., Ly, S. H., Kim, E., et al. (2018) · Nature Genetics

Cancer-related Molecular PathwaysCancer Genomics and Diagnostics

Cited by 556

WRN helicase is a synthetic lethal target in microsatellite unstable cancers

Chan, E. M., Shibue, T., McFarland, J. M., Gaeta, B., Ghandi, M., Dumont, N., Gonzalez, A., McPartlan, J. S., Li, T., Zhang, Y., et al. (2019) · Nature

Genetic factors in colorectal cancerDNA Repair Mechanisms

Cited by 458

Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity

Kinker, G. S., Greenwald, A. C., Tal, R., Orlova, Z., Cuoco, M. S., McFarland, J. M., Warren, A., Rodman, C., Roth, J. A., Bender, S. A., et al. (2020) · Nature Genetics

Single-cell and spatial transcriptomicsCancer Genomics and Diagnostics

Cited by 445

Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition

Wong, G. S., Zhou, J., Liu, J. B., Wu, Z., Xu, X., Li, T., Xu, D., Schumacher, S. E., Puschhof, J., McFarland, J., et al. (2018) · Nature Medicine

Protein Tyrosine PhosphatasesProtein Kinase Regulation and GTPase Signaling

Cited by 266

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

McFarland, J. M., Paolella, B. R., Warren, A., Geiger-Schuller, K., Shibue, T., Rothberg, M., Kuksenko, O., Colgan, W. N., Jones, A., Chambers, E., et al. (2020) · Nature Communications

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 173

A first-generation pediatric cancer dependency map

Dharia, N. V., Kugener, G., Guenther, L. M., Malone, C. F., Durbin, A. D., Hong, A. L., Howard, T. P., Bandopadhayay, P., Wechsler, C. S., Fung, I., et al. (2021) · Nature Genetics

Cancer Genomics and DiagnosticsCRISPR and Genetic Engineering

Cited by 153

Sparse dictionary learning recovers pleiotropy from human cell fitness screens

Pan, J., Kwon, J. J., Talamas, J. A., Borah, A. A., Vazquez, F., Boehm, J. S., Tsherniak, A., Zitnik, M., McFarland, J. M., & Hahn, W. C. (2022) · Cell Systems

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 37

Computational estimation of quality and clinical relevance of cancer cell lines

Trastulla, L., Noorbakhsh, J., Vazquez, F., McFarland, J., & Iorio, F. (2022) · Molecular Systems Biology

Cancer Genomics and DiagnosticsComputational Drug Discovery Methods

Cited by 31