Flagship Pioneering Co-Op Program - ProFound Therapeutics: Bioinformatics Data Engineering Co-Op
Requirements
• Currently pursuing a B.S. or M.S. in Bioinformatics, Computational Biology, Biology, Biochemistry, Computer Science or a related field, and available for a full-time, 4–6 month co-op term. • Python (pandas) and comfort with the Linux command line. • Git, and a habit of writing clear, tested, reproducible code. • Coursework or project experience in genomics or molecular biology, such as RNA-seq, translation, protein or DNA sequence analysis, or proteomics basics. • Clear written communication; you document what you build. • Nextflow, Snakemake, Airflow or another workflow manager, plus Docker. • Exposure to AWS (e.g., S3, EC2, Athena). • Familiarity with Ribo-seq, long-read sequencing or mass spectrometry data (e.g., peptides, PSMs, database search). • Basic statistics, such as differential expression, false discovery rate and multiple-testing correction. • A dashboard or web app you’ve built (e.g., Dash, Streamlit, Shiny), linked from GitHub or a portfolio. • Experience with AI coding assistants (e.g., Claude Code, Copilot, Cursor) on real projects, with a sense of where they help and where they fail. • Exposure to LLM APIs, agents, MCP, or classic ML (e.g., scikit-learn, PyTorch) applied to biological data. • What You’ll Learn and Gain • How production Nextflow pipelines are built, tested and run on the cloud. • How a data catalog (Glue, Athena, Parquet) turns raw omics outputs into queryable resources. • How a computational team supports a drug discovery platform, with exposure to the wet-lab work behind the data. • How to use AI-assisted development responsibly in a regulated, data-sensitive setting: verification, testing, and knowing what data may and may not go to which tools. • A shipped project with your name on it.
Responsibilities
• Run and monitor pipelines. Run Nextflow pipelines for ribosome profiling (Ribo-seq), long-read sequencing and DIA proteomics on AWS Batch. Triage failed jobs and summarize QC with MultiQC and alignment metrics. • Run and monitor pipelines. • Build and validate QC. Flag samples that fail set thresholds. Compare results across GENCODE versions. Write automated checks that catch suspicious or missing experiment data before it reaches downstream scoring. • Build and validate QC. • Analyze proteomics evidence. This includes peptide-to-protein mapping, sequence coverage, FDR-filtered evidence, and comparisons across search engines and experiments. • Analyze proteomics evidence. • Write and test scripts. Use Python and R to parse, filter and summarize outputs (FASTA, GTF, BAM, peptide and protein tables) into Parquet or TSV. Turn exploratory notebooks into reusable, version-controlled code. • Write and test scripts. • Grow the data catalog. Add or update a dataset: ingest it, document its schema and check it with Athena (SQL) queries. • Grow the data catalog. • Build tools for scientists. Prototype a visualization or dashboard (Plotly/Dash, Streamlit or a notebook) that scientists use to review targets and QC results. • Build tools for scientists. • Document and share. Write READMEs and runbooks, and present results in team meetings, including a final co-op presentation. • Document and share. • Example Projects • Example Projects • Benchmark two MS search engines on the same dataset and report where they agree and where they disagree. • Build a Ribo-seq QC report that flags samples failing periodicity or mapping thresholds. • Add a new QC view to a scientist-facing dashboard, from requirements through deployment. • Ingest and document a new biological annotation resource in the data catalog.
Benefits
• Build alongside founders. You’ll work inside the same hypothesis-driven process Flagship uses to conceive and launch first-in-category companies. • Build alongside founders. • This can be the start of a longer story. Strong co-ops are considered for future opportunities across Flagship and its portfolio companies, not just for this one role. • This can be the start of a longer story. • Work alongside people who left the safe path. Your colleagues are scientists, engineers, and operators who chose to build something new rather than join something already established. • Work alongside people who left the safe path • Take on real ownership. You're contributing to ventures that are still being defined. Your work can shape real decisions, not just support them. • Take on real ownership. • Be paid like the contributor you are. Compensation reflects the real work you take on. • Be paid like the contributor you are. • Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. • equal employment opportunity • The pay range for this role is $25 - $35 per hour. This role is a short-term engagement that is not eligible for health and welfare benefits. Retirement benefits may be available after completing a set number of hours. Compensation and benefits information is based on ProFound's good faith estimate as of the date of publication and may be modified in the future.
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