---
title: 'Senior / Principal Scientist - Translational Modeling & Decision Science at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/senior-principal-scientist-translational-modeling-decision-science-flagship-z5ememq64qcq'
type: 'job'
last_seen: '2026-09-11'
---

# Senior / Principal Scientist - Translational Modeling & Decision Science at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-07-09
- **Last confirmed live:** 2026-09-11
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8624887002?gh_jid=8624887002

## Job description

## About Pioneering Intelligence

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

## About the Role

Pioneering Intelligence (PI) is building AI systems that accelerate translational decision making. This forward-deployed role bridges the gap from capability to impact by leveraging PI technologies to take on translational challenges across Flagship’s therapeutic portfolio, delivering value through programs and business decisions while returning insights that improve the AI platform.

The successful candidate will reduce the scientific uncertainty behind Flagship’s drug development and investment decisions through mechanistic modeling and quantitative analysis.

The individual will work across the portfolio rather than within a single program, taking on diligence questions, milestone decisions, and competitive assessments as they arise, matching analytical rigor to the consequence of each decision, and flagging when one program’s finding is relevant to another. They will also serve as an expert test user for the Applied AI and Engineering teams, feeding field discoveries back as product requirements.

The role owns the credibility of its analyses: transparent uncertainty, defensible assumptions, and results a stakeholder can carry into their own decision. The role also owns the identification of opportunities to close comprehension and trust gaps associated with complex agentic work products.

## Responsibilities

Translational Prediction & Decision Support

- Produce quantitative opinions across decision types and scenarios (due diligence, milestone and program decisions, competitive and what-if analyses): decompose claims into testable components, evaluate against evidence, and deliver conclusions on the decision’s timeline
- Deliver translational predictions with stated confidence and boundary conditions for milestone decisions (target engagement, therapeutic window, modality feasibility, competitive differentiation)
- Quantify probability of pharmacological success by integrating uncertainty across compound, mechanism, and disease dimensions
- Translate scientific complexity into recommendations stakeholders can carry and defend in their own decisions, not just a number to take on trust

Cross-Portfolio Pattern Recognition

- Carry insight between programs, flagging when one company’s translational risk is relevant to another
- Prioritize where predictive science creates the most decision value at each development milestone
- Define context-of-use for each engagement: what question, what decision, what credibility standard, what cost of being wrong
- Match analytical rigor to decision consequence using regulatory credibility concepts (ICH M15, FDA MIDD) adapted for internal decisions

Feedback Loop into the Agentic Platform

- Translate field discoveries into product requirements for the Applied AI and Engineering teams
- Provide domain-expert signal: define what good predictions look like, curate ground truth from real engagements, and evaluate output quality
- Prototype novel modeling approaches to prove feasibility and define acceptance criteria before handoff
- Review autonomous outputs for scientific correctness and feed failure cases back as regression tests and custom benchmarks/evaluations

Scientific Standards & Execution

- Personally execute problems that require expert judgment: novel biology, new modalities, or high-consequence analyses
- Set quality standards on every engagement: rigorous evidence evaluation, transparent uncertainty quantification, reproducible methodology
- Communicate translational results in Flagship-internal forums and, where appropriate, external ones
- Deliver structured retrospectives on engagements (scientific outcome, decision informed, value created, collaborator feedback)

## Qualifications

Required

- PhD in a life sciences discipline with quantitative experience, or in a quantitative life sciences discipline (pharmacometrics, systems pharmacology, computational biology, biomedical engineering, or equivalent) with 3 to 7 years of industry experience with strong knowledge of physiology, molecular biology, and immunology
- Demonstrated expertise building mechanistic models for drug development decisions across multiple therapeutic areas
- Ability to translate scientific complexity into recommendations for non-technical decision-makers with excellent communication skills and composure under pressure
- Proficiency in Python scientific computing (scipy, numpy, pandas) and numerical ODE integration
- Experience operating across multiple concurrent programs and decision types

## Preferred

- Experience applying frontier AI and LLM tools to drug development decisions
- Translational breadth across drug modalities (small molecule, biologic, gene therapy, novel platforms)
- Familiarity with regulatory credibility frameworks (ICH M15, FDA MIDD) and their application to internal decision-making
- Experience in venture-backed or platform-company environments where analysis supports investment decisions

## ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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](https://www.flagshippioneering.com).

At Flagship, we accept impossible missions to enable bigger leaps. Our [core values](https://www.flagshippioneering.com/values) guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its 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.

## #LI-MB1

The salary range for this role is $146,000 - $236,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence'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 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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