Anupam Chattopadhyay

Aneuploidy Spectrum Analysis as a Primer for Copy Number Profiling of Cancer Cells

AStra is a framework for aneuploidy profiling of cancer data that assesses suitability for copy number analysis, showing high accuracy in identifying aneuploidy spectra and ploidy levels.

Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line

The paper develops HiCNAtra to correct Hi-C contact maps by integrating copy number variation information, improving accuracy over existing methods.

Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes

CNAtra detects and distinguishes large-scale and focal copy number alterations in low-coverage cancer genomes with high precision and recall.

Parsers, Data Structures and Algorithms for Macromolecular Analysis Toolkit (MAT): Design and Implementation

The paper introduces MAT, a toolkit for parsing and analyzing macromolecular data files, offering faster and more accurate parsing with new data structures and algorithms.