Yosef, Nir

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Street, K., Risso, D., Fletcher, R. B., Das, D., Ngai, J., Yosef, N., Purdom, E., & Dudoit, S. (2018) · BMC Genomics

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 3,159

Deep generative modeling for single-cell transcriptomics

Lopez, R., Regier, J., Cole, M. B., Jordan, M. I., & Yosef, N. (2018) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 2,530

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

Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells

Kleinewietfeld, M., Manzel, A., Titze, J., Kvakan, H., Yosef, N., Linker, R. A., Muller, D. N., & Hafler, D. A. (2013) · Nature

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

Cited by 1,394

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

Induction and molecular signature of pathogenic TH17 cells

Lee, Y., Awasthi, A., Yosef, N., Quintana, F. J., Xiao, S., Peters, A., Wu, C., Kleinewietfeld, M., Kunder, S., Hafler, D. A., et al. (2012) · Nature Immunology

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

Cited by 1,174

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., et al. (2022) · Science

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 1,056

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

Wu, C., Yosef, N., Thalhamer, T., Zhu, C., Xiao, S., Kishi, Y., Regev, A., & Kuchroo, V. K. (2013) · Nature

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

Cited by 1,022

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

The epigenetic landscape of T cell exhaustion

Sen, D. R., Kaminski, J., Barnitz, R. A., Kurachi, M., Gerdemann, U., Yates, K. B., Tsao, H.-W., Godec, J., LaFleur, M. W., Brown, F. D., et al. (2016) · Science

T-cell and B-cell ImmunologyCancer Immunotherapy and Biomarkers

Cited by 986

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 942

A Python library for probabilistic analysis of single-cell omics data

Gayoso, A., Lopez, R., Xing, G., Boyeau, P., Valiollah Pour Amiri, V., Hong, J., Wu, K., Jayasuriya, M., Mehlman, E., Langevin, M., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 789

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

Xu, C., Lopez, R., Mehlman, E., Regier, J., Jordan, M. I., & Yosef, N. (2021) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 691

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

Revealing the vectors of cellular identity with single-cell genomics

Wagner, A., Regev, A., & Yosef, N. (2016) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 632

Mapping single-cell data to reference atlases by transfer learning

Lotfollahi, M., Naghipourfar, M., Luecken, M. D., Khajavi, M., Büttner, M., Wagenstetter, M., Avsec, Ž., Gayoso, A., Yosef, N., Interlandi, M., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 602

Joint probabilistic modeling of single-cell multi-omic data with totalVI

Gayoso, A., Steier, Z., Lopez, R., Regier, J., Nazor, K. L., Streets, A., & Yosef, N. (2021) · Nature Methods

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

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

Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

Wagner, A., Wang, C., Fessler, J., DeTomaso, D., Avila-Pacheco, J., Kaminski, J., Zaghouani, S., Christian, E., Thakore, P., Schellhaass, B., et al. (2021) · Cell

T-cell and B-cell ImmunologyPsoriasis: Treatment and Pathogenesis

Cited by 524

MultiVI: deep generative model for the integration of multi-modal data

Ashuach, T., Gabitto, M. I., Jordan, M. I., & Yosef, N. (2021) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 385

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

Molecular recording of mammalian embryogenesis

Chan, M. M., Smith, Z. D., Grosswendt, S., Kretzmer, H., Norman, T. M., Adamson, B., Jost, M., Quinn, J. J., Yang, D., Jones, M. G., et al. (2019) · Nature

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 364

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

DestVI identifies continuums of cell types in spatial transcriptomics data

Lopez, R., Li, B., Keren-Shaul, H., Boyeau, P., Kedmi, M., Pilzer, D., Jelinski, A., Yofe, I., David, E., Wagner, A., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 276