Nir Hacohen

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.

The paper identifies immune hubs in lung cancer that are associated with better responses to PD-1-blockade immunotherapy and contain stem-like CD8 T cells.

The paper uses Perturb-seq to systematically study 1,130 E3 ligases and their roles in inflammatory responses in dendritic cells, revealing co-functional modules and genetic interactions.

The paper identifies two distinct gene programs associated with disease tolerance and resistance in influenza virus infection using mouse strain data.

The paper identifies causal genetic variants in autoimmune diseases by combining allele-specific reporter assays with chromatin accessibility data, showing their impact on gene expression and T cell function.

This study identifies molecular and immune features associated with response to anti-PD-(L)1 therapy in NSCLC using a cohort of 393 patients.

The paper develops DNA- and RNA-based models combining immune and tumor features to predict outcomes of checkpoint inhibition in melanoma.

The paper uses plasma proteomics to identify tissue-specific cell death and cell-cell interaction mediators in severe COVID-19 patients, linking them to survival outcomes and viral infection effects.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

The paper uses the ABC Model to map enhancer-gene regulation across 131 cell types and tissues, linking GWAS variants to disease genes, particularly in IBD.

Cumulus is a cloud-based framework for analyzing large-scale sc/snRNA-seq data, improving efficiency and scalability while maintaining result quality.

MAUDE improves analysis of sorting-based CRISPR screens by quantifying guide RNA effects on gene expression and estimating statistical significance.

Seven single-cell and single-nucleus protocols run side by side on the same cell lines, PBMCs and mouse cortex, analysed through one pipeline: 10x Chromium led the high-throughput methods.

The paper identifies genetic variants influencing isoform usage in the anti-viral response, revealing ERAP2's role in balancing selection and influenza-specific regulation.

GeNets provides a platform to compare genomic networks using machine learning and allows analysis of genetic and RNA sequencing data.

This paper establishes a protocol for preserving and analyzing single-cell transcriptomes from cryopreserved renal tissue and urine samples in lupus nephritis studies.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

The paper proposes the Human Cell Atlas project to catalog all human cell types through molecular profiling and connects this data with classical cellular descriptions.

This paper systematically surveys X chromosome inactivation across human tissues using transcriptomic and genomic data, finding that XCI is generally uniform but shows heterogeneity and identifies new escape genes with sex-biased expression.