Ramya Raviram

The paper shows cohesin collisions maintain ordered nucleosome architecture at CTCF sites and promoters, independent of CTCF occupancy or cohesin levels.

The paper develops scG2P to jointly capture DNA mutations and mRNA transcripts in single cells, revealing clonal architectures and phenotypes in aged esophageal tissue.

This paper develops SMART-PTA for single-cell whole-genome and transcriptome sequencing, revealing clonal evolution in aged human esophageal tissue over 70 years.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper identifies new therapeutic targets in CRLF2-overexpressing B-ALL by analyzing TF-gene regulatory interactions using network inference and experimental validation.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.

The paper demonstrates a two-step mechanism of PRC2-mediated repressive domain formation through nucleation sites and long-range spreading of H3K27me2/3.

The paper introduces 4Tran, a method to study transposon interactions in the genome, revealing their role in chromatin organization and gene regulation.

The paper uses single nucleus ATAC-seq to analyze chromatin accessibility in mouse forebrain development, identifying cell-type-specific regulatory sequences and transcriptional regulators.

The paper introduces a method to identify multi-loci chromatin interactions using 4C-seq data and demonstrates its application to Tcrb and Igk enhancer interactions.

This paper introduces 4C-ker, a method that improves the reproducibility of identifying genome-wide interactions from 4C-Seq data by accounting for signal biases and varying resolution.