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Author Details

Nir Yosef
Center for Computational Biology, University of California berkeley
1986
148
51
Emma Lundberg (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37735568Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.Nat Methods2024
37735568Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.Nat Methods2024
36927151Theoretical guarantees for phylogeny inference from single-cell lineage tracing.Proc Natl Acad Sci U S A2023
37938000Hepatitis C virus infects and perturbs liver stem cells.mBio2023
37808807Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies.bioRxiv2023
37580604Single-cell multiomic analysis of thymocyte development reveals drivers of CD4<sup>+</sup> T cell and CD8<sup>+</sup> T cell lineage commitment.Nat Immunol2023
38076815ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data.bioRxiv2023
36754020Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.Cell Metab2023
37386189MultiVI: deep generative model for the integration of multimodal data.Nat Methods2023
37192164An empirical Bayes method for differential expression analysis of single cells with deep generative models.Proc Natl Acad Sci U S A2023
36927151Theoretical guarantees for phylogeny inference from single-cell lineage tracing.Proc Natl Acad Sci U S A2023
37808807Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies.bioRxiv2023
38076815ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data.bioRxiv2023
37580604Single-cell multiomic analysis of thymocyte development reveals drivers of CD4<sup>+</sup> T cell and CD8<sup>+</sup> T cell lineage commitment.Nat Immunol2023
37938000Hepatitis C virus infects and perturbs liver stem cells.mBio2023
37192164An empirical Bayes method for differential expression analysis of single cells with deep generative models.Proc Natl Acad Sci U S A2023
37386189MultiVI: deep generative model for the integration of multimodal data.Nat Methods2023
36754020Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.Cell Metab2023
34462589Mapping single-cell data to reference atlases by transfer learning.Nat Biotechnol2022
35523183Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.Cell2022
35449415DestVI identifies continuums of cell types in spatial transcriptomics data.Nat Biotechnol2022
35820420Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs.Curr Biol2022
35497495Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision.Cell Rep Methods2022
36070768Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling.Immunity2022
35549406Cross-tissue immune cell analysis reveals tissue-specific features in humans.Science2022
35982664NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.bioRxiv2022
35858747Identifying cell state-associated alternative splicing events and their coregulation.Genome Res2022
35475224PeakVI: A deep generative model for single-cell chromatin accessibility analysis.Cell Rep Methods2022
35979364Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation.Front Immunol2022
35315433Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.Nat Commun2022
35045305CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels.Cell Rep2022
34462589Mapping single-cell data to reference atlases by transfer learning.Nat Biotechnol2022
34965963Mucosal Vaccination with Cyclic Dinucleotide Adjuvants Induces Effective T Cell Homing and IL-17-Dependent Protection against <i>Mycobacterium tuberculosis</i> Infection.J Immunol2022
35179948Batf-mediated epigenetic control of effector CD8<sup>+</sup> T cell differentiation.Sci Immunol2022
35132262A Python library for probabilistic analysis of single-cell omics data.Nat Biotechnol2022
35121805Systems-based approaches to study immunometabolism.Cell Mol Immunol2022
35549406Cross-tissue immune cell analysis reveals tissue-specific features in humans.Science2022
35475224PeakVI: A deep generative model for single-cell chromatin accessibility analysis.Cell Rep Methods2022
35497495Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision.Cell Rep Methods2022
35820420Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs.Curr Biol2022
35523183Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.Cell2022
35858747Identifying cell state-associated alternative splicing events and their coregulation.Genome Res2022
35449415DestVI identifies continuums of cell types in spatial transcriptomics data.Nat Biotechnol2022
36070768Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling.Immunity2022
35982664NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.bioRxiv2022
35979364Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation.Front Immunol2022
35132262A Python library for probabilistic analysis of single-cell omics data.Nat Biotechnol2022
35045305CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels.Cell Rep2022
35315433Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.Nat Commun2022
35179948Batf-mediated epigenetic control of effector CD8<sup>+</sup> T cell differentiation.Sci Immunol2022
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Collaborators

Aviv Regev
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Eytan Ruppin
National Cancer Institute
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Roded Sharan
Tel Aviv University
Co-authored papers 15
Alex K Shalek
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Co-authored papers 11
Nadav Ahituv
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Nir Hacohen
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Michael B Cole
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Weizmann Institute of Science
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Manuel Garber
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Chun Jimmie Ye
University of California san francisco
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Nir Friedman
Co-authored papers 3
Karl R Clauser
Co-authored papers 2
Steven A Carr
Broad Institute of MIT and Harvard
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Clary B Clish
Broad Institute of MIT and Harvard
Co-authored papers 2
Vikram Agarwal
University of Washington
Co-authored papers 2
Liana F Lareau
Co-authored papers 2
Taha Y Taha
Gladstone Institutes
Co-authored papers 2
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 2
Iswar K Hariharan
University of California berkeley
Co-authored papers 2
Release 1.2