Pragati Upadhyay

About

Computational biologist with over 3 years of experience in multi-omics data analysis, statistical modeling, and biomarker discovery. Experienced in large clinical-trial NGS datasets, translational research, and cross-functional collaboration to support precision diagnostics and therapy development.

Experience

• Computational Biologist II
  Ferris lab, Lineberger Comprehensive Cancer Center
  Jul 2025 – Present
• Bioinformatics Analyst
  Ferris lab, UPMC Hillman Cancer Center
  Aug 2023 – Jul 2025
• Computational Biology Co-op
  Obsidian Therapeutics
  Jan 2023 – Mar 2023
• Graduate Research Assistant
  Computational Chemistry lab, Northeastern University
  Aug 2022 – Jan 2023
• Director of Academic Affairs
  Graduate Biotechnology and Bioinformatics Association, Northeastern University
  Jul 2022 – Apr 2023

Education

• Master of Science
  Northeastern University
  Bioinformatics · Sep 2021 – May 2023
• Bachelor of Science
  Vikram University
  Biotechnology · Aug 2017 – Sep 2020

Skills

• SQL
• Git
• Python
• Linux
• AWS
• Docker
• Bash
• Excel
• Azure
• R
• HPC
• Slurm
• Variant Calling
• Differential Gene Expression
• Pathway Enrichment
• Pseudotime
• Clonal Analysis
• Gene Regulatory Network
• Receptor Ligand Interaction
• Correlation
• Rna Fusion Detection
• Survival Analysis
• Nf-Core
• Nextflow
• Gatk
• Star
• Salmon
• Samtools
• Fastqc
• Trimmomatic
• Fastp
• Bowtie
• Deseq2
• Edger
• Trinity
• Bioconductor
• Cell Ranger
• Seurat
• Scanpy
• Screpertoire
• Pyscenic
• Scmalignantfinder
• Cellchat
• Conda
• Singularity

📚 Publications

• Response-associated T cell programs and regimen-specific biomarkers of response to neoadjuvant nivolumab plus ipilimumab or relatlimab · 2026
• TCR determinants correlative to major pathological responses in HNSCC patients treated with dual immune checkpoint inhibitors ↗ · 2026
• Development of a clinical assay to guide patient therapy in HPV-associated head and neck cancer ↗ · 2026
• Tumoral and systemic immune correlates of response to concurrent pembrolizumab and chemoradiotherapy in resected high-risk head and neck squamous cell carcinoma · 2026
• Differential impact of TIM-3 ligands on NK cell function ↗ · 2025
• Conventional and Regulatory CD4+ T Cell Programs Shape Clinical Response to Doublet Neoadjuvant Immunotherapy · 2025
• Tim-3 regulates tumor-infiltrating Treg function and survival, limiting antitumor immunity · 2025