Shalek, Alex K.

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell

Single-cell and spatial transcriptomicsInnovative Microfluidic and Catalytic Techniques Innovation

Cited by 7,110

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science

Single-cell and spatial transcriptomicsGlioma Diagnosis and Treatment

Cited by 5,063

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science

Single-cell and spatial transcriptomicsCancer Immunotherapy and Biomarkers

Cited by 4,944

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., et al. (2015) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 3,159

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 2,232

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

Jerby-Arnon, L., Shah, P., Cuoco, M. S., Rodman, C., Su, M.-J., Melms, J. C., Leeson, R., Kanodia, A., Mei, S., Lin, J.-R., et al. (2018) · Cell

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

Cited by 1,429

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 1,190

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

van Galen, P., Hovestadt, V., Wadsworth II, M. H., Hughes, T. K., Griffin, G. K., Battaglia, S., Verga, J. A., Stephansky, J., Pastika, T. J., Lombardi Story, J., et al. (2019) · Cell

Acute Myeloid Leukemia ResearchSingle-cell and spatial transcriptomics

Cited by 1,164

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,000

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding, J., Adiconis, X., Simmons, S. K., Kowalczyk, M. S., Hession, C. C., Marjanovic, N. D., Hughes, T. K., Wadsworth, M. H., Burks, T., Nguyen, L. T., et al. (2020) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 871

Dynamic regulatory network controlling TH17 cell differentiation

Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., et al. (2013) · Nature

Gene Regulatory Network AnalysisPsoriasis: Treatment and Pathogenesis

Cited by 682

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

Single-cell genomics unveils critical regulators of Th17 cell pathogenicity

Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell

Psoriasis: Treatment and PathogenesisT-cell and B-cell Immunology

Cited by 575

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Gifford, C. A., Ziller, M. J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., Shalek, A. K., Kelley, D. R., Shishkin, A. A., Issner, R., et al. (2013) · Cell

Pluripotent Stem Cells ResearchEpigenetics and DNA Methylation

Cited by 435

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., Jay DaleyKeyser, A., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., et al. (2014) · Nature

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 356

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Menon, M., Mohammadi, S., Davila-Velderrain, J., Goods, B. A., Cadwell, T. D., Xing, Y., Stemmer-Rachamimov, A., Shalek, A. K., Love, J. C., Kellis, M., et al. (2019) · Nature Communications

Single-cell and spatial transcriptomicsRetinal Development and Disorders

Cited by 331

Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer

Dilly, J., Hoffman, M. T., Abbassi, L., Li, Z., Paradiso, F., Parent, B. D., Hennessey, C. J., Jordan, A. C., Morgado, M., Dasgupta, S., et al. (2024) · Cancer Discovery

Pancreatic and Hepatic Oncology ResearchProtein Kinase Regulation and GTPase Signaling

Cited by 308

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

Pepe-Mooney, B. J., Dill, M. T., Alemany, A., Ordovas-Montanes, J., Matsushita, Y., Rao, A., Sen, A., Miyazaki, M., Anakk, S., Dawson, P. A., et al. (2019) · Cell Stem Cell

Liver physiology and pathologyHippo pathway signaling and YAP/TAZ

Cited by 266

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Chevrier, N., Mertins, P., Artyomov, M. N., Shalek, A. K., Iannacone, M., Ciaccio, M. F., Gat-Viks, I., Tonti, E., DeGrace, M. M., Clauser, K. R., et al. (2011) · Cell

Immune Response and Inflammationinterferon and immune responses

Cited by 179

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Genshaft, A. S., Li, S., Gallant, C. J., Darmanis, S., Prakadan, S. M., Ziegler, C. G. K., Lundberg, M., Fredriksson, S., Hong, J., Regev, A., et al. (2016) · Genome Biology

Single-cell and spatial transcriptomicsAdvanced Proteomics Techniques and Applications

Cited by 175

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

Tu, A. A., Gierahn, T. M., Monian, B., Morgan, D. M., Mehta, N. K., Ruiter, B., Shreffler, W. G., Shalek, A. K., & Love, J. C. (2019) · Nature Immunology

Single-cell and spatial transcriptomicsT-cell and B-cell Immunology

Cited by 128

Functional compensation precedes recovery of tissue mass following acute liver injury

Walesky, C. M., Kolb, K. E., Winston, C. L., Henderson, J., Kruft, B., Fleming, I., Ko, S., Monga, S. P., Mueller, F., Apte, U., et al. (2020) · Nature Communications

Liver physiology and pathologyDrug-Induced Hepatotoxicity and Protection

Cited by 103

Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip

Bein, A., Kim, S., Goyal, G., Cao, W., Fadel, C., Naziripour, A., Sharma, S., Swenor, B., LoGrande, N., Nurani, A., et al. (2021) · Frontiers in Pharmacology

3D Printing in Biomedical ResearchSARS-CoV-2 and COVID-19 Research

Cited by 83