Nir Hacohen

The paper develops a computational framework to minimize CD8⁺ T cell immunogenicity in designed proteins while preserving function, using a de novo luciferase as a model.

This study shows folate deprivation impairs CD8+ T cell function by disrupting cell surface glycosylation, and increasing folate uptake enhances T cell anti-tumor activity.

This study defines the single-cell landscape of Class II lupus nephritis and identifies fibroblast transcriptional programs and chronicity index as potential predictors of kidney outcomes.

The paper identifies spatially distinct macrophage-fibroblast interactions in lupus nephritis that drive myofibroblast heterogeneity and fibrosis.

This study identifies Dusp5 and Zfp219 as key regulators of age-related T cell dysfunction using CRISPR screens and shows their potential as therapeutic targets.

This paper introduces a high-throughput single-cell RNA isoform sequencing method using sequencing-by-expansion (SBX) and the CUDLL algorithm, achieving high accuracy and enabling isoform-level analysis across cell types.

The paper shows that CRTC, not phosphorylated CREB1, drives cAMP-induced transcription across multiple cell types, challenging the canonical model of CREB1 activation.

The paper identifies two distinct CD8 T cell gene expression programs in HBV infection that correlate with viral control and functional cure.

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

The paper identifies Trim28 as a regulator of CD8 T cell differentiation in tumors using clonally-resolved CRISPR screens and shows its role in maintaining TCF7+ stem-like cells while impairing effector differentiation.

The paper presents a machine learning challenge to predict gene perturbation effects on T cell differentiation, finding that feature representation from perturbational data improves performance and validating top genes experimentally.

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze myeloid cell dynamics in lupus nephritis, showing shifts in immune responses linked to disease progression.

The paper identifies distinct genetic mechanisms for early (nuclear) and late (cellular) RNA eQTL by comparing their genomic localization and functional effects across tissues.

The paper shows UV exposure causes misfolded melanosomal proteins to aggregate, contributing to skin pigmentation disorders and melanocyte dysfunction.

This study identifies a novel CD8+ TIL subset that uses lymphotoxin and IFN pathways to kill cancer cells, linking LTB expression to clinical response in melanoma.

The paper constructs a single-cell splicing atlas of human CD8 T cells and identifies isoform-specific immune checkpoints that enhance effector function and tumor control.

A single-cell atlas of blood and tissue samples from lupus nephritis patients and healthy controls identifies stromal and immune populations, including scar-associated macrophages, which correlate with disease activity.

This study uses single-cell image-based CRISPR screens to identify host factors regulating Ebola virus infection, revealing new therapeutic targets like UQCRB and STRAP.

This study develops a zebrafish model of mucosal melanoma by activating an oncogene and inactivating tumor suppressors, revealing that internal melanocytes give rise to tumors with distinct transcriptional and chromatin features.

This study shows that targeting CD38 improves T cell function and restores response to immunotherapy in melanoma models.

The paper identifies CREB5 as a driver of immunotherapy resistance in melanoma by promoting collagen matrix deposition, which activates LAIR1 signaling on immune cells.

The paper identifies activated lymphocyte phenotypes in individuals at risk for rheumatoid arthritis using mass cytometry and develops an immunophenotype score to distinguish these individuals from controls.

This study compares the immunological effects of photon and proton radiation therapy in cancer patients, finding that proton therapy preserves T cell diversity and may improve survival.

The paper identifies regulators of STING trafficking through genome-wide screening and characterizes their functional impact on STING signaling.

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

DSMBind predicts binding energy and designs nanobodies without experimental data, achieving performance comparable to supervised models.

This paper develops a platform to model and manipulate human microglial states in vitro using single-cell RNA sequencing and genetic tools, identifying disease-associated transcriptional signatures.

The paper creates a high-resolution cellular atlas of healthy and injured kidney cell states and niches using single-cell and spatial technologies, identifying molecular signatures and pathways related to kidney injury.

This paper introduces MAS-ISO-seq, a method to boost throughput of long-read RNA sequencing for isoform discovery, showing improved detection of differentially spliced genes and cell clustering in T cells.