Charles P. Fulco

Rewriting regulatory DNA to dissect and reprogram gene expression

The paper introduces Variant-FlowFISH to measure the effects of DNA sequence variants on gene expression, identifies regulatory mechanisms, and benchmarks predictive models.

Cohesin-mediated 3D contacts tune enhancer-promoter regulation

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

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

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.

Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity

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.

Compatibility logic of human enhancer and promoter sequences

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: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

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.

Genome-wide maps of enhancer regulation connect risk variants to disease genes

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.

Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes

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

Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations

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

CRISPR-SURF: Discovering regulatory elements by deconvolution of CRISPR tiling screen data

CRISPR-SURF deconvolves CRISPR tiling screen data to identify functional regulatory elements across CRISPR-Cas, CRISPRi, and CRISPRa experiments.