N. Yosef

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The paper profiles immune cell RNA and protein expression across tissues and age to identify tissue-specific and age-related immune signatures.

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids

The paper uses ACE2-overexpressing airway organoids to show NF-κB inhibitor alpha is upregulated during SARS-CoV-2 infection and its reduced function increases viral infection.

Hepatitis C Virus Infects and Perturbs Liver Stem Cells

This study identifies liver stem cells as targets of HCV infection, showing their transcriptional reprogramming and role in liver damage and cancer risk.

Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution

The paper tracks tumor evolution in a mouse model using lineage tracing and single-cell RNA-seq, revealing plasticity, fitness-associated programs, and stereotypical evolutionary trajectories.

Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data

The paper introduces TreeVAE, a probabilistic framework to reconstruct unobserved ancestral cellular states from single-cell lineage tracing and transcriptomics data, showing improved performance over benchmarks.

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

The paper uses single-cell lineage tracing and RNA-seq to identify diverse metastatic behaviors and their drivers in lung cancer xenografts in mice.

Induction of a colitogenic phenotype in Th1 cells depends on IL-23R signaling

This study shows IL-23R signaling enables Th1 cells to acquire a colitogenic phenotype, distinct from Th17 cells, and identifies CD160 as a key regulator.

Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

This study identifies Batf's role in regulating effector CD8+ T cell differentiation through transcriptional and epigenetic mechanisms using genome-scale profiling.

Mucosal vaccination with cyclic-di-nucleotide adjuvants induces effective T cell homing and IL-17 dependent protection against M. tuberculosis infection

This study shows mucosal vaccination with CDN adjuvants induces T cells that home to lungs and provide IL-17-dependent protection against M. tuberculosis.

Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions

This study shows oleic acid enhances FoxP3 Treg stability and suppressive function through FAO-driven OXPHOS, with implications for MS pathology.

Polyamine Metabolism Regulates the T Cell Epigenome Through Hypusination

This study shows that polyamine metabolism, specifically through hypusination, is essential for maintaining T cell subset identity by regulating the epigenome and transcriptional programs.

Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway

The paper identifies the polyamine pathway as a regulator of Th17/Treg balance, showing its impact on inflammation and T cell phenotype.

Deep Generative Models for Detecting Differential Expression in Single Cells

This paper introduces deep generative models for differential expression detection in scRNA-seq, showing improved performance over existing methods.

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

This study compares single-cell transcriptomes of blood and cerebrospinal fluid leukocytes in multiple sclerosis, identifying compartment-specific changes in cell types and transcriptional diversity.