---
title: 'Senior Machine Learning Scientist at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/senior-machine-learning-scientist-flagship-pioneering-inc-cambridge-ftjr2gwbdkcr'
type: 'job'
last_seen: '2026-09-04'
---

# Senior Machine Learning Scientist at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-07-01
- **Last confirmed live:** 2026-09-04
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8609661002?gh_jid=8609661002

## Job description

Position Summary:

We are looking for a Machine Learning Scientist to build AI and machine learning systems that turn complex biological data into actionable scientific insight. You will work at the intersection of ML, genomics, causal biology, and target discovery. The role includes building models, agentic AI workflows, systems that help automate analysis, reasoning, and decision support, and AI assisted tools that help connect genotype, cell state, perturbation, phenotype, and disease mechanism. This is a hands-on role for someone who enjoys writing clear, reliable code, uses modern AI tools to move faster, and wants their work to shape real biological and therapeutic decisions.

Responsibilities:

- Build ML models for genomic, single-cell, perturbation, and phenotype data.
- Develop agentic AI workflows that help scientists analyze data, test hypotheses, and make better decisions.
- Use AI coding tools to accelerate development while keeping code reliable, readable, tested, and reproducible.
- Train and fine tune foundation models, language models, and representation learning methods for target discovery.
- Model relationships between genotype, cell state, perturbation response, causal biology, and disease.
- Collaborate closely with computational scientists, experimental biologists, software engineers, and target discovery teams.
- Communicate results clearly, including model assumptions, limitations, and next steps.

Qualifications:

You do not need to meet every item to apply. Strong candidates may come from academia, industry, open-source work, or hands-on research.

- PhD, Master’s degree, or equivalent experience in machine learning, computer science, computational biology, genomics, bioinformatics, statistics, engineering, or a related field.
- Strong Python coding skills and experience building practical Deep Learning ML systems.
- Experience using AI coding tools, coding assistants, LLM-based workflows, or agentic development tools.
- Experience training, evaluating, or applying ML models to complex real-world data.
- Depth in one or more of: biomedical foundation models, agentic AI, Perturb-seq, single-cell genomics, genotype–phenotype modeling, causal inference, perturbation modeling, or large-scale biological datasets.
- Evidence of technical depth through papers, thesis work, open-source projects, industry projects, or substantial hands-on applied research.

Values and Behaviors:

- Encourage respectful disagreement and cultivate open-minded, ego-free interactions to continuously push each other towards excellence
- Seek out diverse perspectives; practice active listening and genuine curiosity to ensure all contributions are valued, regardless of source
- Recognize the impact of your behavior, language and attitudes, and strive for balanced, meaningful exchanges that enhance mutual growth and understanding in all interactions
- Use a company-first mindset to guide decision-making; prioritize team over individual success
- Take calculated risks and challenge convention in the quest for exceptional outcomes

About Quotient:

Quotient Therapeutics is a privately-held, early stage company developing breakthrough medicines informed by natural somatic genetic diversity present in patients. Through our work in somatic genomics, we are forging a new status quo for biopharma research and development across a broad pipeline of internal and partnered programs.

The company was founded by Flagship Pioneering, an innovative enterprise that conceives, creates, resources, and grows first-in-category life sciences companies. Flagship Pioneering has created over 100 groundbreaking companies over the past twenty years, all of which are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna (MRNA), Generate Biomedicines, Sana Biotechnology (SANA), Tessera Therapeutics, Evelo Biosciences (EVLO), Indigo Agriculture, Seres Therapeutics (MCRB), and Syros Pharmaceuticals (SYRS).

Quotient Therapeutics and Flagship Pioneering are 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.

Recruitment & Staffing Agencies:

Quotient Therapeutics (“Quotient”) and Flagship Pioneering (“FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Quotient, FSP or their employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, 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 privacy@flagshippioneering.com.

## About Flagship Pioneering, Inc.

## Company Overview
- **One-liner**: Flagship Pioneering is a life sciences venture creation firm that conceives, creates, and capitalizes breakthrough bioplatform companies in biotechnology, health, and sustainability.
- **Entity Type**: Private (Venture Creation Firm)
- **Headquarters**: Cambridge, Massachusetts, United States
- **Founded**: 2000
- **Founders**: Noubar Afeyan (Co-Founder & CEO)

## Core Business
- **Primary industry/industries**: Biotechnology Research, Life Sciences Venture Creation, Company Incubation
- **Target customers**: B2B / B2G – partners with academic institutions, pharma companies, and investors; also acts as an employer for scientists, entrepreneurs, and corporate builders
- **Mission or purpose statement**: “To harness the 21st century's most powerful technological forces for good to deliver a better future for all.”

## Products & Services
Flagship does not sell products directly; its offerings are the companies it creates and the innovation platform it operates.
- **Innovation Platform**: A systematic, institutionalized process to identify “unreasonable” scientific questions, test them rigorously, and spin out independent companies that develop therapeutics, diagnostics, agricultural technologies, and more.
- **Portfolio Companies**: Over 120 companies founded, including Moderna, Generate:Biomedicines, Inari Agriculture, Tessera Therapeutics, Lila Sciences, and others. Each is a separate enterprise with its own products (e.g., mRNA vaccines, gene-editing tools, AI-driven drug discovery).

## Market Standing
- **Valuation/Market Cap**: Not publicly disclosed (privately held)
- **Key Metric**: Annual revenue of approximately $800 million (2025/2026 estimate) and 620 employees (+9.7% YoY growth)
- **Notable Investors/Partners**: Flagship is itself an investor and partner; key collaborations include AWS (to accelerate drug discovery), Harvard Medical School, Broad Institute, and multiple top-tier biopharma companies. Portfolio company Moderna is a publicly traded giant.
- **Growth Signals**: 78 active job postings (+50% quarterly), recent formation of Terion (digital agriculture infrastructure) and Serif Biomedicines (modified DNA platform), and expanded presence in Europe and Asia.

## Competitive Advantages
- **Unique Model**: Combines scientific exploration, company creation, and capital investment under one roof – “a way that is largely without precedent”
- **Deep Talent Pool**: Exceptional network of scientist-entrepreneurs and company builders; top hires from MIT, Harvard, Biogen, Novartis, and Pfizer
- **Track Record**: Over two decades of founding transformational companies (e.g., Moderna’s COVID‑19 vaccine), demonstrating repeatable innovation
- **Process-Driven**: Systematic methodology for turning “what‑if” questions into patentable bioplatforms, reducing risk compared to ad‑hoc startup creation

## Strategic Focus
- **Current priorities**: Expanding AI/machine learning integration across drug discovery and life sciences (highlighted by AWS collaboration); entering preemptive health and medicine; advancing sustainable agriculture and climate solutions; growing international operations (UK, Singapore, Canada, Switzerland, Japan)
- **Direction for growth**: Launching new platform companies at a steady cadence (e.g., Terion, Serif in 2026); deepening expertise in computational protein design, modified DNA, and gene editing

## Why Work Here
- **Culture**: “Brave and bold organization of creative-thinkers with insurgent mindsets” – emphasis on fearlessness, mentorship, and teamwork across science and business
- **Work Environment**: Headquarters in Cambridge, MA with 5 US offices; roles span research, strategy, finance, and operations; hybrid/remote flexibility varies by role
- **Notable Perks**: Opportunity to work on world-changing science (e.g., COVID‑19 vaccine, gene editing) alongside top scientists and company builders; strong compensation (salary range example: Sr. Associate ~$68K, ML Engineer ~$122K; overall comp rating 3.7/5)
- **Engineering/Science Culture**: Heavy investment in R&D (15% of workforce in research), cutting-edge tools (Cryo‑EM, AI/ML), and a process that encourages bold leaps

## Sources
1. [flagshippioneering.com](https://www.flagshippioneering.com/)
2. [flagshippioneering.com/about](https://www.flagshippioneering.com/about)
3. [flagshippioneering.com/join](https://www.flagshippioneering.com/join)
4. [flagshippioneering.com/join/roles](https://www.flagshippioneering.com/join/roles)
5. [linkedin.com/company/flagship-pioneering](https://www.linkedin.com/company/flagship-pioneering)

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