Nir Yosef

Berkeley College — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

73h-index33.2kcitations309works9.22yr avg
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Research Topics

Single-cell and spatial transcriptomics(129), T-cell and B-cell Immunology(57), Immune Cell Function and Interaction(57), Genomics and Chromatin Dynamics(36), Cell Image Analysis Techniques(34)

Publications306 total

Aging-Associated Microbiota Drives Treg Dysfunction via TNF Signaling
2025Open Access
Metabolic zonation and characterization of tissue slices with spatial transcriptomics
2025Open Access
A functional CAR-T cell atlas to unravel regulatory mechanisms of CAR-T therapies
Blood·2025Open Access
Benchmarking cell type and gene set annotation by large language models with AnnDictionary
Nature Communications·2025· 4 citedOpen Access
Deep generative modeling of sample-level heterogeneity in single-cell genomics
Nature Methods·2025· 7 citedOpen Access
An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products
2025Open Access
Preselection CD4 <sup>+</sup> CD8 <sup>+</sup> thymocytes modulate TCR responsiveness following TCRβ selection
2025Open Access
CytoVI: Deep generative modeling of antibody-based single cell technologies
2025Open Access
Scvi-hub: an actionable repository for model-driven single-cell analysis
Nature Methods·2025· 2 citedOpen Access
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age
Nature Immunology·2025· 13 citedOpen Access
Aging-Associated Microbiota Drives Treg Dysfunction via TNF Signaling
2025Open Access
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing
Systematic Biology·2025· 2 citedOpen Access
Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs
Cell stem cell·2025· 4 cited
Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution
2025Open Access
High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer
Science·2025· 10 citedOpen Access
High-resolution spatial mapping of cell state and lineage dynamics <i>in vivo</i> with PEtracer
2025· 3 citedOpen Access
MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq
Nucleic Acids Research·2025· 17 citedOpen Access
scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics
2025· 1 citedOpen Access
The glycolytic reaction PGAM restrains Th17 pathogenicity and Th17-dependent autoimmunity
Cell Reports·2025Open Access
ZEB2 is a master switch controlling the tumor-associated macrophage program
Cancer Cell·2025· 23 cited
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Frequent Co-authors

Aviv Regev(19), Vijay K. Kuchroo(8), Hongkun Park(7), Romain Lopez(6), Alex K. Shalek(6), Jellert T. Gaublomme(6), Chuan Wu(6), Chenling Xu(6), Ido Amit(6), Jeffrey Regier(5), Michael I. Jordan(5), Nir Hacohen(5), Sheng Xiao(5), Adam Gayoso(5), Tal Ashuach(5), Fabian J. Theis(5), Allon Wagner(5), Davide Risso(4), John Ngai(4), Elizabeth Purdom(4)