Staff Bioinformatics Scientist — Epigenomics & 3D Genome Architecture

Summary

9 years specialising in chromatin biology and 3D genome organisation. Designed and led epigenomics programmes at AstraZeneca and the Salk Institute, covering ATAC-seq, ChIP-seq, Hi-C, and CUT&RUN at scale. Built an internal Snakemake framework handling 500+ epigenomics samples per quarter on Azure. Strong publication record in high-impact journals; invited reviewer for Genome Biology and Nature Genetics.

Experience

Staff Scientist, Epigenomics — AstraZeneca (2020–Present)

• Built a unified Snakemake epigenomics platform (ATAC-seq, ChIP-seq, CUT&RUN, Hi-C) deployed on Azure HPC; processes 500+ samples/quarter with full audit trails for regulatory submissions.
• Identified novel super-enhancer rewiring in KRAS-mutant NSCLC using H3K27ac HiChIP; findings advanced 2 compounds to IND.
• Mentored 4 junior scientists; established team-wide code review and reproducibility standards.

Postdoctoral Fellow — Salk Institute (Ecker Lab) (2017–2020)

• Generated and analysed single-nucleus methylome + chromatin accessibility data across 45 human brain regions; contributed to BRAIN Initiative Cell Census.
• Developed chromloop, an R package for chromatin loop calling from Hi-C data (Bioconductor, 180 downloads/month).

Selected Publications

• Venkataraman P. et al. “Super-enhancer remodelling drives oncogenic transcription in KRAS-mutant lung cancer.” Cancer Cell, 2023.
• BICCN Consortium (contributing author). “A multimodal cell census of the human brain.” Nature, 2021.
• Venkataraman P. et al. “chromloop: precise Hi-C loop calling with variable resolution.” Bioinformatics, 2019.

Code Quality Notes

Snakemake pipelines ship with conda environment locks, containerised rule environments (Singularity), and integration tests. R packages follow Bioconductor submission guidelines with full vignettes and unit tests via testthat. All GitHub repos use branch protection and squash-merge PRs.