Professional Summary:

Computational biologist with 9+ years of experience in multi-omics analysis, specializing in single-cell, spatial, TCR, epitope, and bioinformatics pipeline development. Experienced in developing single cell, spatial and bulk multi-omics bioinformatics pipelines in neuro-oncology, immune ageing, autoimmunity, population genomics, & rare disease. Seeking to contribute my skills in biotech for oncology, biomarker discovery, or therapeutic target identification.

Key Skills

• Single-Cell: scRNA, scTCR, CITESeq, scATAC, Multiome, BEAM-T, TetTCR
• Spatial: Xenium, Visium, MERFISH, Cyclic IF, CODEX
• Bulk: Whole Genome Sequencing, Transcriptomics, Epigenomics
• Workflow Optimization: Nextflow, Docker, Singularity & RShiny
• Programming: R, Python, Shell scripting; HPC (Slurm, SGE, LSF)
• Machine learning: scikit-learn, PyTorch
• Cloud Computing: AWS, MS-Azure, GCP
• Collaboration: Extensively worked with clinicians, wet-lab, dry-lab
• Industry Consultant: Consultant for a startup Genomiki Solutions
• Academic Mentorship: Guided postdoc and PhD students
• Leadership: Lead computational team for India 1000 Genome Project
• Version Control: Git, Github

Professional Experience

Computational Biologist, VoyantBio, San Francisco Aug’25-Now
• Integrated pan cancer immune single cell and spatial dataset to identify the biomarkers to improve immunotherapy response.

Post-Doctoral Fellow, UCSF, San Francisco Jun’24-Aug’25
• Analyzed snRNA, ATAC, and spatial (Visium & Xenium) transcriptomics to identify therapeutic targets in SHH medulloblastoma
• Developing lineage-tracing methodologies to track tumor evolution using CRISPR barcodes
• Foundation model (scGPT) fine-tuned using >100 paired scRNA brain cancer metastasis

Post-Doctoral Fellow, Mayo Clinic, Rochester Aug’21–May’24
(Currently Collaborator)
• Characterized antigen-specific T-cell in aging and vaccine using CITESeq, BEAM-T & ATACseq
• Performed scRNA, scmultiome,scTCR and bulk RNA to identify clonal diversity in naïve CD4 T cells of Aortitis patients
• Integrated single-cell and spatial (Visium, CODEX, and multiplexed Cycif) to study immune cell crosstalk in autoimmune disorders

Graduate Research Fellow CSIR-IGIB, New Delhi July’16 – July’21
• Led bioinformatics analysis team for 1,000+ Indian Genome Sequencing Project, focusing on rare disease variants
• Developed workflows for SARS-CoV-2 variant tracking using Illumina and Nanopore sequencing
• Variant prioritization in ~300 primary immunodeficiency disorder patients using genome sequencing

Selected Publications:

Full list on Google Scholar
• Sturmlechner I#, Jain A#, et al. Aging trajectories of memory CD8+ T cells differ by their antigen specificity. Nature Communications (2025)
• Sato Y, Jain A, et al. Stem-like CD4 T cells in perivascular tertiary lymphoid structures sustain autoimmune vasculitis. Science Translation Medicine (2023)
• Jain A#, Bhoyar R#, et al. IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. Nucleic Acid Research (2021)
• Zhang H#, Okuyama H#, Jain A#, PREX1 improves homeostatic proliferation to maintain a naive CD4+ T cell compartment in older age. JCI Insight (2024)
#-co-first author