Joseph Nasser

The paper derives a mathematical model explaining the ABC Score formula for enhancer-gene prediction and shows its limitations in capturing non-additive effects.

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The paper introduces a method to prioritize causal genes for complex traits by integrating GWAS data with gene expression and biological data, achieving high precision in gene-trait pair identification.

The paper shows how KLF4 interacts with SWI/SNF to increase chromatin accessibility at enhancers under laminar shear stress, promoting endothelial homeostasis and suppressing inflammation.

The paper links SNPs to genes using functionally informed strategies, revealing enhancer-related and master-regulator genes contribute to autoimmune disease heritability.

The paper develops a combined SNP-to-gene linking strategy (cS2G) to improve the identification of disease-causing genes and assess disease omnigenicity using GWAS data.

The paper measures enhancer-promoter compatibility in human cells using a high-throughput assay, finding a multiplicative model with some class-specific preferences.

HyPR-seq sensitively quantifies up to 100 chosen genes in single cells, achieving high sensitivity for individual transcripts and reducing costs compared to whole-transcriptome scRNA-seq.

The paper improves deep learning SNP annotations for complex diseases by integrating them with SNP-to-gene linking strategies and gradient boosting, showing increased informativeness for autoimmune diseases.

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.

The paper identifies germline genetic variants associated with clonal hematopoiesis of indeterminate potential (CHIP) using whole genome sequences from the TOPMed program.

The paper analyzes 41 diseases and traits to show transposable elements contribute uniquely to disease heritability, with older elements and SINEs showing specific enrichment patterns.

The paper introduces CRISPRi-FlowFISH to perturb enhancers and an Activity-by-Contact model to predict enhancer-gene regulatory connections.

The paper introduces a method to detect directional effects of transcription factor binding on disease risk using GWAS data and applies it to identify new causal genes and mechanisms.