Pioneering Medicines: Bioinformatics Co-Op

This position is open exclusively to current Northeastern University Co-Op students.

January 2027 to June 2027. This is a full- time, 40 hours per week position with 5 days in office.

Pioneering Medicines, Flagship Pioneering’s therapeutics innovation hub, partners with world-class scientists to launch and build breakthrough biotechnology companies. Our bioinformatics team turns multi-omic and clinical data into insights that drive target discovery, translational research, and pipeline decisions across a portfolio of novel therapeutics companies.

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE's "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World's Most Innovative Companies. Learn more about Flagship at

Welcome to Flagship Pioneering Co-Op Program for the cohort dreaming big and taking courageous leaps. You’ll join fellow peers across our ecosystem of companies and learning firsthand how we build first-in-category companies. You’ll have access to enrichment sessions , a dedicated professional development track , and a mentor that help guide you toward your next step. By the end, you will carry on a meaningful project outcome , a genuine network , and a front-row view of how Flagship pioneer new ventures that change the world.

As a Bioinformatics Co-op, you will work alongside computational and bench scientists to analyze large-scale biological datasets supporting active drug discovery programs. You’ll gain hands‑on experience with single-nucleus (snRNA-seq) analysis and disease genomics, while learning core bioinformatic processes and building skills spanning genomics, data science, and pipeline development across multiple therapeutic programs.

The co‑op will lead a project analyzing and understanding quality control (QC) for single-nucleus RNA-seq (snRNA-seq) data, defining and applying QC metrics and filtering criteria to ensure data integrity ahead of downstream analysis. This project is embedded within an active Pioneering Medicines therapeutic program and will also serve as a capability build for the company, establishing reusable snRNA‑seq QC standards and workflows for future programs.

• Analyze single-nucleus (snRNA‑seq) and single‑cell datasets to characterize cell populations relevant to disease biology.
• Support disease genomics analyses, including variant interpretation and genotype‑phenotype exploration, to inform target identification and validation.
• Build, adapt, and run computational pipelines (e.g., RNA‑seq, single‑nucleus/single‑cell, WGS/WES) using tools such as Nextflow, Snakemake, or custom scripts.
• Apply statistical and machine learning methods to identify patterns in multi‑omic and experimental data.
• Query and integrate data from internal and public databases (e.g., TCGA, GTEx, CCLE, GEO).
• Create clear visualizations and…