About the role#
As a Bioinformatics Data Engineering Co-Op, you will work on production pipelines and datasets within an industry drug discovery setting. You will own a scoped project from start to finish, such as a QC dashboard, a pipeline benchmark, or a new annotation resource. You will receive code review and mentorship from the team while working directly with the scientists who use the tools you build.
What you'll do#
- Run and monitor Nextflow pipelines for ribosome profiling, long-read sequencing, and DIA proteomics on AWS Batch.
- Triage failed jobs, summarize QC with MultiQC, and flag samples that fail set thresholds.
- Build and validate QC processes and compare results across GENCODE versions.
- Write automated checks to catch missing or suspicious experiment data.
- Analyze proteomics evidence, including peptide-to-protein mapping and sequence coverage.
- Write and test scripts in Python and R to parse and summarize data outputs.
- Turn exploratory notebooks into version-controlled, reusable code.
- Grow the data catalog by ingesting, documenting, and querying datasets with SQL.
- Prototype visualizations or dashboards for scientists to review targets.
- Document your work in READMEs and runbooks and present results in team meetings.
What you'll need#
- Currently pursuing a B.S. or M.S. in Bioinformatics, Computational Biology, Biology, Biochemistry, Computer Science, or a related field.
- Availability for a full-time, 4-6 month co-op term.
- Proficiency in Python (pandas) and comfort with the Linux command line.
- Experience with Git and a habit of writing clear, tested, reproducible code.
- Coursework or project experience in genomics or molecular biology.
- Clear written communication skills.
- Preferred experience includes basic R, SQL, Nextflow or other workflow managers, Docker, and AWS (S3, EC2, Athena).
- Familiarity with Ribo-seq, long-read sequencing, mass spectrometry data, and basic statistics.
- A portfolio featuring a dashboard or web app you have built.
- Experience with AI coding assistants and exposure to LLM APIs, agents, or classic machine learning applied to biological data.
Location & details#
- This position is based in Watertown, Massachusetts.
- The role is a full-time, 40-hour per week commitment.
- The work modality is hybrid.
- The available terms are Winter 2027 and Summer 2027.
- This position is paid.
About Flagship Pioneering
Flagship Pioneering is a biotechnology firm based in Cambridge, Massachusetts. Founded in 2000, the company focuses on inventing and building platform companies that develop products for human health and sustainability. It has originated more than 100 scientific ventures since its inception. The current ecosystem includes over 40 companies, such as Indigo Agriculture and Generate:Biomedicines.
How to get in at Flagship Pioneering
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