Director, Modeling and Simulation

What if... We could harness the power of Flagship’s scientific platforms and create novel treatment options that benefit more patients, sooner?

About Flagship Pioneering:

Flagship Pioneering is a scientific innovation engine that originates and builds platform companies and products that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps, exponentially accelerating scientific progress in human health, sustainability, and beyond. As part of our modeling and simulation team, you will partner across the Flagship ecosystem, from newly founded ventures to later-stage portfolio companies, applying mechanistic modeling approaches to help translate bold scientific ideas into transformative therapies.

Position Summary:

We are seeking a highly motivated individual to provide leadership and hands-on support for modeling efforts (PK/PD/QSP) across Flagship’s diverse drug discovery portfolio. The qualified candidate is expected to support internal and external due diligence work, provide guidance for Flagship platform companies to accelerate timelines from Lead ID to DC and to apply innovative modeling approaches to inform early feasibility concepts. As programs advance, the role extends through Lead OP and pre-IND, integrating modeling workstreams into cross-functional development strategy and, in collaboration with clinical teams, supporting the design and interpretation of emerging clinical data. We are seeking individuals with deep subject matter expertise who are analytical, goal-oriented and committed to maintaining the highest scientific and ethical standards. Strong communication skills and comfort to utilize AI-supported modeling workflows in a dynamic, cross-functional team environment are highly desirable.

Key Responsibilities:

Work with cross-functional development teams and platform companies to identify modeling needs, model complexity and required data to

help de-risk program questions related to safety and efficacy

inform TCP and/or TPP

provide guidance for pre-clinical in vitro and in vivo studies

test MoA-related hypothesis

conduct competitor analysis

support clinical translation of pre-clinical data including FiH dose predictions

inform target prioritization

support regulatory interactions (e.g., FDA meetings, IND-enabling packages) through model-informed drug development (MIDD) approaches

Develop QSP and PK/PD models (either internally or with CROs) for various modalities (small molecules, mono-clonal antibodies, multi-specifics, cell therapy, LNPs) and therapeutic areas (obesity, cardio-vascular, oncology, immunology, rare diseases)

Provide guidance to early-stage Flagship companies to help accelerate their timelines from Lead ID to DC

Utilize AI-supported modeling workflows to provide end-to-end modeling support including model scoping, model development, model calibration and analysis to accelerate decision-making for due diligence and early feasibility analysis

Ensure that supporting infrastructure (software, methods, external consulting support, etc.) is efficient and meets all required standards.

Manage (Director) a small team of modeling scientists and CROs, including scientific oversight, budget, and timeline accountability for externalized model development

Education and Experience:

PhD. in pharmacology, engineering sciences, (bio-)physics or applied mathematics with 5+ years of experience in QSP and/or PK/PD modeling; 8+ years, including direct experience managing scientists and/or CRO relationships, is expected for the Director level

Advanced experience in QSP modeling workflows, deep understanding of mechanistic, physiologically-based modeling principles and biological subject matter expertise in at least one disease area; familiarity with population PK/PD (e.g., nonlinear mixed-effects, Bayesian methods) and experience with AI-supported and/or agentic modeling workflows desirable

Programming skills (e.g., R, Python, Matlab), hands-on modeling experience using Simbiology, NONMEM, Monolix, Pumas, or similar software packages

Experience supporting drug discovery programs including due diligence and early feasibility assessments

Excellent oral and written communication skills with the ability to work in a multidisciplinary team with colleagues and collaborators representing diverse backgrounds

Track record of representing scientific work externally (e.g., publications, conference presentations, scientific advisory interactions) is a plus

About Flagship

Flagship Pioneering is a scientific innovation engine that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps in human health, sustainability, and beyond.

What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our team of scientists, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and create breakthroughs for the benefit of people and planet. 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 named four times to Fast Company’s annual list of the World’s Most Innovative Companies.

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.

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 [email protected].

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, co