Noam Shoresh F

A multiplexed, target-based phenotypic screening platform using CRISPR interference in Mycobacterium abscessus

This paper introduces a CRISPRi-based PROSPECT platform for drug discovery in M. abscessus, identifying new compound targets and revealing unexpected susceptibility to isoniazid.

Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis

This paper introduces PCL analysis to predict small molecule mechanisms of action in Mycobacterium tuberculosis using PROSPECT data, achieving high sensitivity and precision in MOA prediction.

Multi-locus CRISPRi targeting with a single truncated guide RNA

This paper develops a CRISPRi approach using truncated guides to screen multiple transcription factor binding sites, showing they can disrupt enhancer activity and repress transcription factor binding.

Multiplexed screen identifies a Pseudomonas aeruginosa-specific small molecule targeting the outer membrane protein OprH and its interaction with LPS

The paper identifies a Pseudomonas aeruginosa-specific small molecule, BRD1401, that targets OprH and disrupts its interaction with LPS, increasing membrane fluidity.

Perturbation-Specific Transcriptional Mapping for unbiased target elucidation of antibiotics.

This paper introduces PerSpecTM, a method to predict antibiotic mechanisms of action by comparing transcriptional responses of new molecules to known perturbations, demonstrating its effectiveness with three new anti-Pseudomonas aeruginosa compounds.

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

The paper introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

Detecting sample swaps in diverse NGS data types using linkage disequilibrium

Crosscheck detects mislabeled samples in NGS data by analyzing linkage disequilibrium, correcting errors in 1% of ENCODE datasets.

An Optimized Competitive-Aging Method Reveals Gene-Drug Interactions Underlying the Chronological Lifespan of Saccharomyces cerevisiae

The paper introduces an optimized competitive-aging method to identify gene-drug interactions affecting yeast chronological lifespan, revealing a link between protein glycosylation and metformin-induced lifespan extension.

A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues

This study analyzes RNA-seq data from 6,700 normal tissues to identify somatic mutations and their association with age and tissue proliferation, finding tissue-specific cancer mutation hotspots.

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

The paper uses gene expression data and GWAS summary statistics to identify disease-relevant tissues and cell types by detecting heritability enrichments in gene-specific expression regions.