Flagship Pioneering

Principal Scientist, Translational Modeling & Decision Science

Flagship Pioneering$179K — $236K *
Pharmaceuticals & Biotech
Less than 5 years of experience
Job Overview by Ladders

Qualifications

  • PhD in life sciences or quantitative life sciences with strong physiology knowledge
  • Expertise in mechanistic modeling for drug development
  • Ability to simplify scientific concepts for non-technical audiences
  • Proficient in Python for scientific computing and ODE integration
  • Experience managing multiple programs and decision types

Responsibilities

  • Produce quantitative opinions for various decision scenarios
  • Deliver translational predictions with confidence levels
  • Quantify pharmacological success probabilities
  • Translate scientific complexity into actionable recommendations
  • Identify translational risks across programs
  • Prioritize predictive science for decision value
  • Translate field discoveries into product requirements

Benefits

  • Healthcare coverage
  • Annual incentive program
  • Retirement benefits
  • Broad range of other benefits
Full Job Description
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 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

#LI-MB1

The salary range for this role is $179,000 - $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.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

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