Pioneering Medicines: Bioinformatics Co-Op

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 34,000 - 48,000; Full time

Job summary

Flagship Pioneering is seeking a Bioinformatics Co-op for Northeastern University students to work January 2027 through June 2027 in Cambridge, MA. The role emphasizes analyzing large-scale biological data, developing pipelines, and contributing to drug-discovery programs with guidance from a multidisciplinary team.

You will gain hands-on experience with single-nucleus analyses and disease genomics, while learning core bioinformatic processes and best practices in a collaborative, office-based

Qualifications

• Currently enrolled in an undergraduate or Master’s program in bioinformatics, computational biology, computer science, statistics, genetics, or a related field.
• Proficient in Python or R, with Unix/Linux and Git knowledge.
• Familiarity with genomics or biological data types (NGS, single-cell, proteomics) preferred.

Responsibilities

• 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.
• Build, adapt, and run computational pipelines (RNA-seq, single-nucleus/single-cell, WGS/WES) using Nextflow, Snakemake, or custom scripts.

Skills

Python or R

Unix/Linux

Git

Communication skills

Education

Undergrad or Master's in Bioinformatics / computational biology / CS / statistics

Tools

Nextflow

Snakemake

Docker

Job description

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

Work Period

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

About the Company

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.

About Flagship Pioneering

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 www.flagshippioneering.com.

Flagship Pioneering Co-Op Program

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.

About the Role

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.

Project Focus

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.

What You’ll Do

• 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 summaries to communicate findings to interdisciplinary project teams.
• Document methods and code to ensure reproducibility and support downstream use by the team, while learning core bioinformatic processes and best practices from the broader team.

Who You Are

• Currently enrolled in an undergraduate or Master’s program in bioinformatics, computational biology, computer science, statistics, genetics, or a related field.
• Proficient in Python or R, with working knowledge of Unix/Linux and version control (Git).
• Familiarity with genomics or biological data types (NGS, single‑cell, proteomics) preferred.
• Exposure to statistics, machine learning, or workflow tools (Nextflow, Snakemake, Docker) is a plus.
• Strong problem‑solving skills, curiosity, and the ability to work independently and in a team.
• Clear written and verbal communication skills.

What We Offer

• Build alongside founders. You’ll work inside the same hypothesis‑driven process Flagship uses to conceive and launch first‑in‑category companies.
• 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.
• 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.
• Take on real ownership. You’re contributing to ventures that are still being defined. Your work can shape real decisions, not just support them.
• Be paid like the contributor you are. Compensation reflects the real work you take on.

Equal Opportunity Statement: 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.

Compensation: 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 Flagship Pioneering’s good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI‑assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

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 Pioneering Medicines's good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI‑assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].