Ramil Nurtdinov

EPIraction creates an enhancer-gene interaction atlas using H3K27ac ChIP-Seq data and GWAS SNPs to annotate candidate target genes.

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

This study identifies genetic variants associated with urinary phthalate metabolite levels in children through GWAS and CNV analysis.

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 identifies weak CEBPA binding in humans as a cause of slower B cell transdifferentiation compared to mice, linked to Alu repeat expansions.

The paper introduces a paired-guide RNA CRISPR-Cas9 system to identify protein-coding and lncRNA genes involved in human B-cell to macrophage transdifferentiation, identifying 26 potential novel genes.

The paper tracks transcriptomic and epigenomic changes during human pre-B cell to macrophage transdifferentiation, finding coordinated chromatin state transitions and gene activation patterns.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.