Director, Modeling and Simulation

Flagship Pioneering, Inc. · Cambridge, MA USA

  • Senior
  • Full-time
  • $172,000 – $236,500
  • Posted 2026-11-06
  • Confirmed live on 10 November 2026

Apply at Flagship Pioneering, Inc.

Job description

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

Prepare for the interview

Nothing collected for this employer yet. The Blind 75 is what technical screens draw from; practice it here, with a coach, in Java or Python.

More at Flagship Pioneering, Inc.

All open software jobs