ProFound Therapeutics: Bioinformatics Data Engineering Co-Op

Flagship Pioneering Co-Op Program • Cambridge, MA

1d • $25 - $35 • Hybrid

About The Position

ProFound Therapeutics is seeking a Bioinformatics Data Engineering Co-Op to work on production bioinformatics pipelines and datasets in an industry drug discovery setting. With code review and mentorship from the team, the co-op will own a scoped project from start to finish, work directly with scientists who use the resulting tools and data, and present the project to the team. Example projects include developing a QC dashboard, benchmarking a pipeline, adding an annotation resource, or building a statistics module.

The role is part of the Flagship Pioneering Co-Op Program, which offers enrichment sessions, a professional development track, and a mentor. The position is based in Watertown, Massachusetts, and is a full-time, 40-hour-per-week hybrid co-op from January 2027 through June 2027. It is open exclusively to current Northeastern University co-op students.

ProFound Therapeutics discovers novel proteins across the expanded human proteome using its ProFoundry Platform, which integrates protein detection, validation, and computational technologies. The company works with pharmaceutical partners and the Gates Foundation. The co-op will gain hands-on experience with production Nextflow pipelines, cloud-based data catalogs, omics data, and responsible AI-assisted development in a data-sensitive setting.

Requirements

• Currently pursuing a B.S. or M.S. in Bioinformatics, Computational Biology, Biology, Biochemistry, Computer Science, or a related field.
• Available for a full-time, 4–6 month co-op term.
• Python proficiency, including 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, such as RNA-seq, translation, protein or DNA sequence analysis, or proteomics basics.
• Clear written communication and the ability to document work.
• Must be a current Northeastern University Co-Op student.

Nice To Haves

• Basic R.
• SQL.
• Experience with Nextflow, Snakemake, Airflow, or another workflow manager, plus Docker.
• Exposure to AWS, such as S3, EC2, or Athena.
• Familiarity with Ribo-seq, long-read sequencing, or mass spectrometry data, including peptides, PSMs, or database search.
• Basic statistics, such as differential expression, false discovery rate, and multiple-testing correction.
• A dashboard or web app built with Dash, Streamlit, Shiny, or a similar tool, linked from GitHub or a portfolio.
• Experience using AI coding assistants such as Claude Code, Copilot, or Cursor on real projects, with an understanding of their strengths and limitations.
• Exposure to LLM APIs, agents, MCP, or classic machine learning such as scikit-learn or PyTorch applied to biological data.

Responsibilities

• Run and monitor Nextflow pipelines for ribosome profiling (Ribo-seq), long-read sequencing, and DIA proteomics on AWS Batch; triage failed jobs and summarize QC using MultiQC and alignment metrics.
• Build and validate QC checks, flag samples that fail thresholds, compare results across GENCODE versions, and catch suspicious or missing experiment data before downstream scoring.
• Analyze proteomics evidence, including peptide-to-protein mapping, sequence coverage, FDR-filtered evidence, and comparisons across search engines and experiments.
• Write and test Python and R scripts to parse, filter, and summarize FASTA, GTF, BAM, peptide, and protein outputs into Parquet or TSV; convert exploratory notebooks into reusable, version-controlled code.
• Ingest and document datasets in the data catalog, document schemas, and validate data with Athena SQL queries.
• Prototype visualizations or dashboards for scientists to review targets and QC results.
• Write READMEs and runbooks, share results in team meetings, and deliver a final co-op presentation.
• Own a scoped project from start to finish and work directly with scientists who use the resulting tools and datasets.

Benefits

• Professional development track and mentor through the Flagship Pioneering Co-Op Program.
• Potential consideration for future opportunities across Flagship and its portfolio companies for strong co-ops.
• Compensation of $25–$35 per hour.
• Retirement benefits may be available after completing a set number of hours.
• Health and welfare benefits are not available for this short-term engagement.

What This Job Offers

• Job Type: Full-time
• Career Level: Intern
• Education Level: No Education Listed