Abhijit Chakraborty

This study identifies CTCF as a strong G4 DNA binder and shows its role in genome topology and gene expression through chromatin looping and CTCF occupancy.

The paper identifies subERCEs as master transcription factor binding sites that drive early replication timing and transcription in mESCs, functioning as both enhancers and structural chromatin organizers.

This study identifies quorum sensing regulators and NRPS/PKS operons in X. szentirmaii that govern antibiotic production during stationary phase.

The paper uses single-cell transcriptomics to show Evf2 lncRNA guides Dlx5/6UCE to many enhancer-gene guidance sites, with subpopulation-specific effects and long-range gene regulation.

The paper investigates how var2csa influences var gene expression in Plasmodium falciparum by analyzing chromatin structure changes after gene deletion.

ExTraMapper improves transcript-level orthology mapping between human and mouse by identifying more exon and transcript mappings than previous methods.

The paper shows Evf2 RNA regulates gene expression in mouse forebrain by interacting with Sox2 to control enhancer interactions and chromosome topology.

dcHiC identifies significant changes in chromatin compartmentalization across multiple Hi-C datasets, revealing biologically relevant differences in gene regulation and chromatin states.

PresRAT identifies bacterial small-RNA sequences and their targets, predicting 60,518 sRNAs and 2447 targets across 54 and 13 bacterial genomes, respectively.

The paper constructs replication timing networks from human cell types and identifies master regulators and novel trans interactions between transcription factors and RT changes.

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

This study shows TET enzymes enhance Aicda expression by depositing 5hmC at its superenhancer, promoting chromatin accessibility and CSR in B cells.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

This paper develops tools to identify copy number variations and translocations in cancer cells using Hi-C data, finding 105 amplifications, 45 deletions, and 90 translocations in cancer cell lines.