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Bioinformatics | Long-read sequencing | Host-pathogen genomics
Vaishnav P Varma
Project Associate-I at CSIR–Institute of Genomics and Integrative Biology, New Delhi. I build long-read sequencing pipelines and computational tools that turn Oxford Nanopore data into usable answers about infectious disease and the human epigenome.
Research Focus
My current work centers on ONT-based dengue genomic surveillance and SNP-level characterization of ESKAPE pathogens, alongside haplotype-resolved CpG methylation analysis. I'm also interested in integrative multi-omics approaches that connect viral and host biology within the same computational framework.
Selected Work
ONT Dengue Surveillance
End-to-end long-read sequencing workflows for dengue genomic surveillance, using Dorado, minimap2, Clair3, and ARTIC, with downstream clinical cohort analysis.
Maxscriber
A Linux CLI tool for clinical metadata transcription, patient stratification, QC validation, and statistical visualization in ONT dengue cohorts.
HBV Vaccine Design
Designed a multi-epitope Hepatitis B Virus vaccine candidate after screening more than 111,000 protein sequences across 8 genotypes.
Patent: Palm Sap Collection Apparatus
Granted Indian Patent No. 520964 for an apparatus that collects palm sap while restricting bat access, reducing the risk of Nipah virus spillover.