Lead Bioinformatics Engineer
Flagship Pioneering, Inc.4 days ago
Base Salary
$128k - $176k/yr
Responsibilities
- Own and operate the portfolio bioinformatics platform stack, including CodeOcean, Sequera/Nextflow Tower, Tamarind.bio, and related tools.
- Build reusable pipeline templates, starter deployments, and documented workflows for portfolio companies and scientific teams.
- Translate open-source bioinformatics library contributions into deployable, reproducible, and portable workflows.
- Establish standards for genomic data formats, pipeline documentation, code contributions, governance, and reproducibility.
- Guide scientists and informatics teams in independently building and adapting pipelines on the platform.
- Partner with cloud engineering, data engineering, research systems, lab systems, and machine learning teams to integrate bioinformatics workloads into shared platforms.
- Manage genomic and biomedical data access partnerships, including DAC applications, DUAs, renewals, compliance reporting, and dataset onboarding.
- Advise teams on genomics, transcriptomics, multi-omics, computational resources, and bioinformatics best practices.
Requirements
- M.S. or Ph.D. in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field.
- At least 7 years of hands-on bioinformatics engineering experience with production-grade pipeline development and deployment.
- Deep expertise in genomic data types and formats including FASTQ, BAM/CRAM, VCF, BED, HDF5, and AnnData.
- Experience building and operating cloud-native bioinformatics workflows using AWS, Azure, or GCP and workflow managers such as Nextflow, Snakemake, or WDL.
- Strong programming proficiency in Python and/or R, plus shell scripting for pipeline automation.
- Familiarity with public genomic repositories and access/compliance frameworks such as dbGaP, UK Biobank, and TCGA.
- Experience managing external relationships and data access processes, including DUAs, DAC applications, and compliance reporting.
- Preferred experience administering managed bioinformatics platforms, supporting multi-company scientific teams, single-cell and spatial transcriptomics workflows, containerization, orchestration, data governance, cataloging, lineage tracking, and open-source bioinformatics libraries.
- Prior experience in biotechnology, pharmaceutical, or life sciences technology organizations is preferred.
Benefits
- Healthcare coverage, annual incentive program, retirement benefits, and a broad range of additional benefits are offered.
Tech Stack
Categories
Data Engineering
About Flagship Pioneering, Inc.
Flagship Pioneering invents, builds, and finances platform biotechnology companies in human health and sustainability, providing founding science, capital, and operational support to entrepreneurs and researchers. The privately held firm, founded in 2000 and headquartered in Cambridge, MA, has originated more than 100 ventures and maintains an ecosystem of 40+ companies. Notable portfolio companies include Moderna, Denali Therapeutics, Generate:Biomedicines, Indigo Agriculture, and Tessera Therapeutics.