Senior Bioinformatics Engineer — Single-Cell & Spatial Transcriptomics

Summary

7 years building production-grade bioinformatics pipelines for single-cell and spatial transcriptomics. Led computational teams at Broad Institute and Genentech. Contributed to 3 Nature Methods papers on atlas-scale scRNA-seq integration. Strong communicator with experience presenting to both wet-lab teams and C-suite stakeholders.

Experience

Senior Bioinformatics Scientist — Genentech (2021–Present)

• Architected a Nextflow DSL2 pipeline processing 2M+ cells/week on AWS Batch; reduced cost 40% via spot-instance orchestration.
• Led spatial transcriptomics analysis for 3 oncology programs (Visium HD + Xenium), integrating with bulk RNA-seq and proteomics.
• Built reproducible Seurat/Scanpy harmonisation framework adopted across 6 internal teams.

Postdoctoral Associate — Broad Institute (2019–2021)

• Developed scVI-based multi-modal integration method; code released as open-source (1.2k GitHub stars).
• Co-first author on Human Cell Atlas consortium paper (Nature, 2021, cited 800+).

Selected Publications

• Sharma A. et al. “Scalable multi-modal integration for atlas-scale single-cell data.” Nature Methods, 2022.
• HCA Consortium (co-first author). “A single-cell census of human tissues.” Nature, 2021.

Code Quality Notes

GitHub repositories include full CI/CD (GitHub Actions), Docker + Singularity containers for HPC portability, and Nextflow test profiles with nf-test. Documentation via MkDocs with API reference auto-generated from docstrings.