FL104 | Cambridge, MA Principal Translational Modeling and Simulation Scientist

Flagship Pioneering; Cambridge (MA); On-site; USD 140,000 - 180,000; Full time

Job summary

A leading biotechnology company is seeking a Principal Translational Modeling and Simulation Scientist in Cambridge, MA. This role involves developing mathematical models that bridge biology and medicine, guiding drug discovery through advanced computational strategies, and contributing to a collaborative environment focused on innovation in translational science.

Benefits

Access to world-class resources

Collaborative scientific culture

Qualifications

• 12+ years of industry experience required.
• Proven track record in mechanistic models in translational or clinical contexts.
• Strong communication skills to translate complex models into actionable insights.

Responsibilities

• Lead design of quantitative systems pharmacology and related translational mechanistic models.
• Develop modeling frameworks to inform clinical trial design.
• Beta test FL104’s software and provide feedback for performance improvement.

Skills

QSP

PK/PD Modeling

Communication

Education

PhD in systems pharmacology, bioengineering, applied mathematics, or related field

Tools

MATLAB

Monolix

SimBiology

Julia

Python

Git

AWS

Job description

Principal Translational Modeling and Simulation Scientist

Cambridge, MA USA

Flagship Labs 104 (FL104) is a privately held, early-stage company leveraging artificial intelligence and large language models (LLMs) to transform how we reason about complex phenomena. This is a unique opportunity to be at the forefront of scientific innovation, as we leverage cutting-edge advancements in AI and ML to drive breakthroughs in drug discovery and fundamental science.

About Flagship

Flagship Pioneering is a biotechnology 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 .

Position Summary

FL104 is seeking a Principal Translational Modeling Scientist to lead the development of mathematical models that bridge biology and medicine. You will help define and implement computational modeling strategies that integrate data across scales—from molecular and cellular mechanisms to patient-level outcomes. You will also work closely with FL104’s researchers and engineers to identify opportunities to improve our software platform. This role is central to FL104’s mission and offers the opportunity to help shape a novel approach to translational science.

Key Responsibilities

• Lead the design and implementation of quantitative systems pharmacology (QSP), physiology-based pharmacokinetics (PBPK), pharmacokinetics/pharmacodynamics (PKPD), and translational mechanistic models for disease biology and therapeutic response.
• Develop and apply modeling frameworks to prioritize targets, optimize drug properties, and inform clinical trial design.
• Engage with external partners and internal stakeholders to align modeling objectives with therapeutic strategy and guide internal strategy.
• Present modeling results in a clear and impactful way to cross-functional teams, collaborators, and senior leadership.
• Beta test and benchmark FL104’s software to identify and prioritize opportunities to improve performance and user experience and provide feedback to AI researchers and engineers.

Qualifications

• PhD. in systems pharmacology, bioengineering, applied mathematics, or a related field, with 12+ years of industry experience.
• Proven track record in developing and applying mechanistic models in translational or clinical contexts.
• Expertise in QSP, PK/PD modeling, and simulation tools such as MATLAB, Monolix, SimBiology, or Julia.
• Experience managing alliances with multi-disciplinary teams in pharma, biotech, or academic translational research settings.
• Strong communication skills and the ability to translate complex models into actionable insights for diverse stakeholders.

Preferred Qualifications

• Experience contributing to IND-enabling or clinical development programs and leading computational modeling within programs.
• Background in immunology, oncology, or metabolic disease is a plus.
• Experience building and simulating mechanistic models in Python environments.
• Familiarity with hybrid modeling approaches that combine mechanistic models and machine learning.
• Experience with Git, AWS, and collaborating on software projects.

Why Join Us?
FL104 offers you a unique opportunity to:

• Be part of an ambitious and collaborative scientific culture.
• Build a new category of intelligent software systems for translational science.
• Work at the interface of biology, engineering, and AI to shape the future of drug development.
• Join a Flagship-backed venture with access to world-class resources, infrastructure, and mentorship.

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.

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