Nir Yosef

Research interests

Publications

• The scverse project provides a computational ecosystem for single-cell omics data analysis

  Nature Biotechnology · 2023 · 10.1038/s41587-023-01733-8

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

  Nature Biotechnology · 2022 · https://doi.org/10.1038/s41587-021-01206-w

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

  Science · 2022 · https://doi.org/10.1126/science.abl4896

• Cross-tissue immune cell analysis reveals tissue-specific features in humans

  Science · 2022 · https://doi.org/10.1126/science.abl5197

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

  Molecular Systems Biology · 2021 · 10.15252/msb.20209620

• Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

  Cell · 2021 · 10.1016/j.cell.2021.05.045

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

  Nature Methods · 2021 · 10.1038/s41592-020-01050-x

• Mapping single-cell data to reference atlases by transfer learning

  Nature Biotechnology · 2021 · 10.1038/s41587-021-01001-7

• Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis

  Nature Communications · 2020 · 10.1038/s41467-019-14118-w

• Molecular recording of mammalian embryogenesis

  Nature · 2019 · 10.1038/s41586-019-1184-5

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

  BMC Genomics · 2018 · https://doi.org/10.1186/s12864-018-4772-0

• Deep generative modeling for single-cell transcriptomics

  Nature Methods · 2018 · https://doi.org/10.1038/s41592-018-0229-2

• Revealing the vectors of cellular identity with single-cell genomics

  Nature Biotechnology · 2016 · 10.1038/nbt.3711

• The epigenetic landscape of T cell exhaustion

  Science · 2016 · 10.1126/science.aae0491

• CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

  Cell · 2015 · 10.1016/j.cell.2015.10.068

• Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

  Cell · 2015 · 10.1016/j.cell.2015.11.009

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

  Nature · 2014 · 10.1038/nature13437

• The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

  Nature Immunology · 2014 · 10.1038/ni.2834

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

  Nature · 2013 · 10.1038/nature11984

• Dynamic regulatory network controlling TH17 cell differentiation

  Nature · 2013 · 10.1038/nature11981

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

  Nature · 2013 · 10.1038/nature11868

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

  Nature · 2013 · 10.1038/nature12172

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

  Molecular Cell · 2012 · 10.1016/j.molcel.2012.07.030

• Induction and molecular signature of pathogenic TH17 cells

  Nature Immunology · 2012 · 10.1038/ni.2416

• Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

  Cell · 2011 · 10.1016/j.cell.2011.01.004

Current projects

No projects listed.