Abhijit Chakraborty

TL;DR: An integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing is presented and finds SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure.

TL;DR: It is demonstrated that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.

TL;DR: This work assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices, to identify low-quality experiments.

TL;DR: This work characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), to call inter- chromosomal translocations and their boundaries from HiCtrans, and to simulate hi-C data from genomes with desired rearrangements and abnormalities (AveSim) to benchmark the accuracy of the methods.

TL;DR: It is shown that there is a transient reversal of miRNA‐mediated repression during the early phase of the inflammatory response in macrophages, which leads to the protection of cytokine mRNAs from miRNA-mediated repression.