Hybrid Bioinformatics Data Engineer Co-op

Flagship Pioneering; Cambridge (MA); Hybrid; USD 34,000 - 48,000; Full time

Benefits offered by this job

Paid co-op program

Job summary

Flagship Pioneering offers a Bioinformatics Data Engineering Co-Op through ProFound Therapeutics. You’ll work on production pipelines and datasets, with code review and mentorship from the team. You’ll own a scoped project from start to finish and present it to the team at the end.

The Co-Op is designed to complement your academic training with hands-on experience in production bioinformatics and data engineering in an industry drug discovery setting.

Qualifications

• Currently pursuing a B.S. or M.S. in Bioinformatics, Computational Biology, Biology, Biochemistry, Computer Science or 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.

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.
• Analyze proteomics evidence. This includes peptide-to-protein mapping, sequence coverage, FDR-filtered evidence, and comparisons across search engines and experiments.
• Write and test scripts. Use Python and R to parse, filter and summarize outputs into Parquet or TSV.
• Grow the data catalog. Add or update a dataset and document its schema.

Skills

Python (pandas)

Linux CLI

Git

Communication

Education

B.S./M.S. in Bioinformatics or related field

Co-op availability 4–6 months

Tools

Nextflow

Snakemake

Airflow

Docker

Plotly/Dash

AWS

Job description

Flagship Pioneering offers a Bioinformatics Data Engineering Co-Op through ProFound Therapeutics. You’ll work on production pipelines and datasets, with code review and mentorship from the team. You’ll own a scoped project from start to finish and present it to the team at the end.

The Co-Op is designed to complement your academic training with hands-on experience in production bioinformatics and data engineering in an industry drug discovery setting.