N
Nir Yosef
Researcher at University of California, Berkeley
Publications - 212
Citations - 22154
Nir Yosef is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Gene & Cellular differentiation. The author has an hindex of 48, co-authored 190 publications receiving 15732 citations. Previous affiliations of Nir Yosef include UCB & Brigham and Women's Hospital.
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Journal ArticleDOI
The Human Cell Atlas
Aviv Regev,Aviv Regev,Aviv Regev,Sarah A. Teichmann,Sarah A. Teichmann,Sarah A. Teichmann,Eric S. Lander,Eric S. Lander,Eric S. Lander,Ido Amit,Christophe Benoist,Ewan Birney,Bernd Bodenmiller,Bernd Bodenmiller,Peter J. Campbell,Peter J. Campbell,Piero Carninci,Menna R. Clatworthy,Hans Clevers,Bart Deplancke,Ian Dunham,James Eberwine,Roland Eils,Roland Eils,Wolfgang Enard,Andrew Farmer,Lars Fugger,Berthold Göttgens,Nir Hacohen,Nir Hacohen,Muzlifah Haniffa,Martin Hemberg,Seung K. Kim,Paul Klenerman,Paul Klenerman,Arnold R. Kriegstein,Ed S. Lein,Sten Linnarsson,Emma Lundberg,Emma Lundberg,Joakim Lundeberg,Partha P. Majumder,John C. Marioni,John C. Marioni,John C. Marioni,Miriam Merad,Musa M. Mhlanga,Martijn C. Nawijn,Mihai G. Netea,Garry P. Nolan,Dana Pe'er,Anthony Phillipakis,Chris P. Ponting,Stephen R. Quake,Wolf Reik,Wolf Reik,Wolf Reik,Orit Rozenblatt-Rosen,Joshua R. Sanes,Rahul Satija,Ton N. Schumacher,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Ehud Shapiro,Padmanee Sharma,Jay W. Shin,Oliver Stegle,Michael R. Stratton,Michael J. T. Stubbington,Fabian J. Theis,Matthias Uhlen,Matthias Uhlen,Alexander van Oudenaarden,Allon Wagner,Fiona M. Watt,Jonathan S. Weissman,Barbara J. Wold,Ramnik J. Xavier,Nir Yosef,Nir Yosef,Human Cell Atlas Meeting Participants +81 more
TL;DR: An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.
Journal ArticleDOI
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
Kelly Street,Davide Risso,Russell B. Fletcher,Diya Das,John Ngai,John Ngai,Nir Yosef,Elizabeth Purdom,Sandrine Dudoit +8 more
TL;DR: Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories and infers more accurate pseudotimes than other leading methods.
Journal ArticleDOI
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Alex K. Shalek,Rahul Satija,Xian Adiconis,Rona S. Gertner,Jellert T. Gaublomme,Raktima Raychowdhury,Schraga Schwartz,Nir Yosef,Christine M. Malboeuf,Diana Lu,John J. Trombetta,David Gennert,Andreas Gnirke,Alon Goren,Alon Goren,Nir Hacohen,Nir Hacohen,Joshua Z. Levin,Hongkun Park,Hongkun Park,Aviv Regev,Aviv Regev +21 more
TL;DR: The authors used single-cell RNA-Seq to investigate heterogeneity in the response of bone marrow derived dendritic cells (BMDCs) to lipopolysaccharide (LPS) and found extensive, and previously unobserved, bimodal variation in mRNA abundance and splicing patterns.
Journal ArticleDOI
Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells
Markus Kleinewietfeld,Arndt Manzel,Arndt Manzel,Jens Titze,Jens Titze,Heda Kvakan,Nir Yosef,Ralf A. Linker,Dominik N. Müller,Dominik N. Müller,David A. Hafler,David A. Hafler +11 more
TL;DR: It is shown that increased salt concentrations found locally under physiological conditions in vivo markedly boost the induction of murine and human TH17 cells, which display a highly pathogenic and stable phenotype characterized by the upregulation of the pro-inflammatory cytokines GM-CSF, TNF-α and IL-2.
Journal ArticleDOI
Deep generative modeling for single-cell transcriptomics.
TL;DR: Single-cell variational inference (scVI) is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.