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Computational Biology and Chemistry|November 2, 2025
Introducing feature identification and refinement engine (FIRE) for identifying consistent and informative gene signatureShivam Kumar, Devvrat Pandey, Samrat ChatterjeeComputational Biology and Chemistry|July 7, 2025
TCGAimmunosurv: An R package to identify genes associated with patient survival and immune cell state transitions using TCGA and single-cell RNA-seq dataDevvrat Pandey, Shivam Kumar, Dipanka Tanu Sarmah, et al.Methods (San Diego, Calif.)|November 9, 2024
HistoSPACE: Histology-inspired spatial transcriptome prediction and characterization engineShivam Kumar, Samrat ChatterjeeNPJ Systems Biology and Applications|December 12, 2025
Feature learning augmented with sampling and heuristics (FLASH) improves model performance and biomarker identificationShivam Kumar, Abhinav Agarwal, Samrat ChatterjeeNPJ Systems Biology and Applications|February 24, 2026
Unlocking the potential of computational phenotypic drug discovery: methods, challenges, and future directionsShivam Kumar, Aman Pal, Samrat ChatterjeeComputational and Structural Biotechnology Journal|July 21, 2025
konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction networkShivam Kumar, Abhinav Agarwal, Dipanka Tanu Sarmah, et al.Bioinformatics (Oxford, England)|December 22, 2022
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction networkShivam Kumar, Dipanka Tanu Sarmah, Shailendra Asthana, et al.Computational Biology and Chemistry|February 9, 2024
Exploration of functional relations among differentially co-expressed genes identifies regulators in glioblastomaShivam Kumar, Dipanka Tanu Sarmah, Abhijit Paul, et al.Frontiers in Cellular and Infection Microbiology|June 30, 2025
Emerging RNA-centric technologies to probe RNA-protein interactions: importance in decoding the life cycle of positive sense single strand RNA viruses and antiviral discoverySreemoyee Ghosh, Shivam Kumar, Rohit Verma, et al.Mathematical Biosciences|May 5, 2012
Coupling effect of grazing pressure and nutrient enrichment on system stabilitySamrat ChatterjeePageof 18