Yosef, Nir

Hotspot identifies informative gene modules across modalities of single-cell genomics

DeTomaso, D., & Yosef, N. (2021) · Cell Systems

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 267

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

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

Cole, M. B., Risso, D., Wagner, A., DeTomaso, D., Ngai, J., Purdom, E., Dudoit, S., & Yosef, N. (2019) · Cell Systems

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 173

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Ryu, A. H., Eckalbar, W. L., Kreimer, A., Yosef, N., & Ahituv, N. (2017) · Scientific Reports

Genomics and Chromatin DynamicsBacterial Genetics and Biotechnology

Cited by 139

Use Antibiotics in Cell Culture with Caution: Genome-wide Identification of Antibiotic-Induced Changes in Gene Expression and Regulation

Ryu, A. H., Eckalbar, W. L., Kreimer, A., Yosef, N., & Ahituv, N. (2017) · Scientific Reports

Genomics and Chromatin DynamicsBacterial Genetics and Biotechnology

Cited by 139

A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements

Lopez, R., Nazaret, A., Langevin, M., Samaran, J., Regier, J., Jordan, M. I., & Yosef, N. (2019) · arXiv

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 105

An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

Zhang, H., Madi, A., Yosef, N., Chihara, N., Awasthi, A., Pot, C., Lambden, C., Srivastava, A., Burkett, P. R., Nyman, J., et al. (2020) · Cell Reports

T-cell and B-cell ImmunologyCytokine Signaling Pathways and Interactions

Cited by 91

Enhancing scientific discoveries in molecular biology with deep generative models

Lopez, R., Gayoso, A., & Yosef, N. (2020) · Molecular Systems Biology

Single-cell and spatial transcriptomicsMachine Learning in Bioinformatics

Cited by 82

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

Gong, W., Granados, A. A., Hu, J., Jones, M. G., Raz, O., Salvador-Martínez, I., Zhang, H., Chow, K.-H. K., Kwak, I.-Y., Retkute, R., et al. (2021) · Cell Systems

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 62

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

DeTomaso, D., & Yosef, N. (2016) · BMC Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 58

Deep generative modeling of sample-level heterogeneity in single-cell genomics

Boyeau, P., Hong, J., Gayoso, A., Kim, M., McFaline-Figueroa, J. L., Jordan, M. I., Azizi, E., Ergen, C., & Yosef, N. (2025) · Nature Methods

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 55

Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling

Pawlak, M., DeTomaso, D., Schnell, A., Meyer zu Horste, G., Lee, Y., Nyman, J., Dionne, D., Regan, B. M. L., Singh, V., Delorey, T., et al. (2022) · Immunity

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

Cited by 49

Network-Free Inference of Knockout Effects in Yeast

Peleg, T., Yosef, N., Ruppin, E., & Sharan, R. (2010) · PLoS Computational Biology

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 14

AutoEval Done Right: Using Synthetic Data for Model Evaluation

Boyeau, P., Angelopoulos, A. N., Yosef, N., Malik, J., & Jordan, M. I. (2024) · arXiv

Machine Learning and Data ClassificationMachine Learning and Algorithms

Cited by 1