Judhajeet Ray

The paper uses Perturb-seq to analyze gene knockouts in cancer cell lines, identifying context-specific gene dependencies and transcriptional responses.

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

The paper tests enhancer-promoter compatibility using improved assays, finding that promoter responsiveness, not enhancer rank order, determines activation sensitivity.

PerturbPlan provides an analytical framework to design single-cell CRISPR screens by calculating statistical power and enabling interactive experiment planning.

The paper introduces PReCIS-seq, a nascent RNA assay, to study lineage-specific Pol II activity in mouse skin, revealing mechanisms of gene regulation in adult homeostasis.

This study identifies most distal element-gene interactions have small effect sizes (<10%) using DC-TAP-seq, revealing limitations in prior CRISPR screens and suggesting new model requirements.

The paper identifies causal genetic mechanisms at CAD GWAS loci using CRISPR screens and chromatin analysis, revealing enhancer-gene links and ancestry/sex-specific risk factors.

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

Femto-seq enables targeted DNA sequencing from specific nuclear regions in individual cells using nanoscale photobiotinylation and sequencing.

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.