Regev, Aviv

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J. K., et al. (2020) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 499

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 488

Comparative functional genomics of the fission yeasts

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., et al. (2011) · Science

Fungal and yeast genetics researchGenomics and Phylogenetic Studies

Cited by 484

Molecular logic of cellular diversification in the mouse cerebral cortex

Di Bella, D. J., Habibi, E., Stickels, R. R., Scalia, G., Brown, J., Yadollahpour, P., Yang, S. M., Abbate, C., Biancalani, T., Macosko, E. Z., et al. (2021) · Nature

Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanisms

Cited by 464

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science

Advanced Proteomics Techniques and ApplicationsGene Regulatory Network Analysis

Cited by 460

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

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Lee, M. N., Ye, C., Villani, A.-C., Raj, T., Li, W., Eisenhaure, T. M., Imboywa, S. H., Chipendo, P. I., Ran, F. A., Slowikowski, K., et al. (2014) · Science

interferon and immune responsesImmune Response and Inflammation

Cited by 442

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., et al. (2015) · Cell

Immune Response and InflammationCRISPR and Genetic Engineering

Cited by 440

Autism genes converge on asynchronous development of shared neuron classes

Paulsen, B., Velasco, S., Kedaigle, A. J., Pigoni, M., Quadrato, G., Deo, A. J., Adiconis, X., Uzquiano, A., Sartore, R., Yang, S. M., et al. (2022) · Nature

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 439

Induction and transcriptional regulation of the co-inhibitory gene module in T cells

Chihara, N., Madi, A., Kondo, T., Zhang, H., Acharya, N., Singer, M., Nyman, J., Marjanovic, N. D., Kowalczyk, M. S., Wang, C., et al. (2018) · Nature

T-cell and B-cell ImmunologyCancer Immunotherapy and Biomarkers

Cited by 438

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Hwang, W. L., Jagadeesh, K. A., Guo, J. A., Hoffman, H. I., Yadollahpour, P., Reeves, J. W., Mohan, R., Drokhlyansky, E., Van Wittenberghe, N., Ashenberg, O., et al. (2022) · Nature Genetics

Pancreatic and Hepatic Oncology ResearchSingle-cell and spatial transcriptomics

Cited by 426

The microbiota regulate neuronal function and fear extinction learning

Chu, C., Murdock, M. H., Jing, D., Won, T. H., Chung, H., Kressel, A. M., Tsaava, T., Addorisio, M. E., Putzel, G. G., Zhou, L., et al. (2019) · Nature

Memory and Neural MechanismsGut microbiota and health

Cited by 421

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis

Khajuria, R. K., Munschauer, M., Ulirsch, J. C., Fiorini, C., Ludwig, L. S., McFarland, S. K., Abdulhay, N. J., Specht, H., Keshishian, H., Mani, D. R., et al. (2018) · Cell

RNA and protein synthesis mechanismsHematopoietic Stem Cell Transplantation

Cited by 416

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

A cellular and spatial map of the choroid plexus across brain ventricles and ages

Dani, N., Herbst, R. H., McCabe, C., Green, G. S., Kaiser, K., Head, J. P., Cui, J., Shipley, F. B., Jang, A., Dionne, D., et al. (2021) · Cell

Single-cell and spatial transcriptomicsCerebrospinal fluid and hydrocephalus

Cited by 388

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

Garber, M., Yosef, N., Goren, A., Raychowdhury, R., Thielke, A., Guttman, M., Robinson, J., Minie, B., Chevrier, N., Itzhaki, Z., et al. (2012) · Molecular Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 369

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

Shay, T., Jojic, V., Zuk, O., Rothamel, K., Puyraimond-Zemmour, D., Feng, T., Wakamatsu, E., Benoist, C., Koller, D., Regev, A., et al. (2013) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsBioinformatics and Genomic Networks

Cited by 359

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

A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories

Placido, D., Yuan, B., Hjaltelin, J. X., Zheng, C., Haue, A. D., Chmura, P. J., Yuan, C., Kim, J., Umeton, R., Antell, G., et al. (2023) · Nature Medicine

Machine Learning in HealthcarePancreatic and Hepatic Oncology Research

Cited by 349

The evolution of drug resistance in clinical isolates of Candida albicans.

Ford, C. B., Funt, J. M., Abbey, D., Issi, L., Guiducci, C., Martinez, D. A., Delorey, T., Li, B. Y., White, T. C., Cuomo, C., et al. (2015) · eLife

Antifungal resistance and susceptibilityFungal and yeast genetics research

Cited by 348

Parsing the interferon transcriptional network and its disease associations

Mostafavi, S., Yoshida, H., Moodley, D., LeBoité, H., Rothamel, K., Raj, T., Ye, C. J., Chevrier, N., Zhang, S.-Y., Feng, T., et al. (2016) · Cell

interferon and immune responsesCytokine Signaling Pathways and Interactions

Cited by 337

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 331

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

Jin, X., Simmons, S. K., Guo, A., Shetty, A. S., Ko, M., Nguyen, L., Jokhi, V., Robinson, E., Oyler, P., Curry, N., et al. (2020) · Science

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 317