Bioinformatics Engineer — Metagenomics & Microbiome

Summary

8 years building end-to-end metagenomics platforms for pharma, biotech, and clinical research. Core contributor to the Human Microbiome Project Phase 2 consortium. Led computational microbiome programme at Vedanta Biosciences, supporting 3 IND-enabling studies. Deep expertise in both 16S amplicon and shotgun WMS approaches, de novo assembly, and functional metabolic profiling.

Experience

Principal Bioinformatics Engineer — Vedanta Biosciences (2021–Present)

• Designed GCP-based Nextflow metagenomics platform (Kraken2 + MetaPhlAn4 + HUMAnN3) supporting 3 Phase 1/2 clinical trials; outputs feed directly into regulatory submissions.
• Built BigQuery data warehouse for longitudinal microbiome time-series across 1,200 trial participants; enabled real-time analyst dashboards in Looker.
• Implemented de novo assembly QC pipeline (MEGAHIT → CheckM2 → GTDB-Tk) characterising novel bacterial isolates for the therapeutic pipeline.

Postdoctoral Researcher — Knight Lab, UCSD (2018–2021)

• Contributed core analysis pipelines to HMP2 (iHMP) consortium; processed 10,000+ longitudinal stool samples.
• Published QIIME2 plugin for novel diversity metric (iNEXT-based rarefaction-free alpha diversity); 4,000+ conda installs.

Selected Publications

• Ferretti L. et al. “Longitudinal gut microbiome dynamics predict clinical response to live biotherapeutic products.” Cell Host & Microbe, 2023.
• iHMP Consortium (contributing author). “The Integrative Human Microbiome Project.” Nature, 2019.

Code Quality Notes

Nextflow pipelines pass nf-core linting standards; Docker images pinned by digest, not tag. Python packages use pyproject.toml with ruff linting and pytest-cov enforcing ≥85% coverage. BigQuery schemas versioned in Terraform with automated migration tests in CI.