Director, Explanatory Modeling

Director, Explanatory Modeling – Cell Science

The goal of Allen Institute for Cell Science is to develop a comprehensive and holistic approach to measure, describe, and model cell states and their dynamic changes over time with the ultimate goal of uncovering the fundamental principles of multiscale, multicellular morphogenesis, including how groups of cells organize and achieve collective behaviors essential for life. Our approach encompasses multi-modal data collection including live 3D timelapse imaging, data analysis, theory, and predictions to understand cell states and cell state transitions in human induced pluripotent stem cell models. As a division within the Allen Institute, the Allen Institute for Cell Science uses a team-oriented approach, focusing on accelerating foundational research, developing standards and models, and cultivating new ideas to make a transformational impact on science.

The Allen Institute for Cell Science is seeking a highly motivated and goal-oriented Director of Explanatory Modeling, to lead the development and implementation of multiscale mechanistic models that explain how cellular events emerge from underlying processes— for example, by iterating between and integrating agent-based approaches, bottom-up simulations, continuum models, and theory. This role offers a unique opportunity for a generalist to contribute to The Institute’s transformative vision for cellular biology as described in our recent Perspectives article in Cell. The Director will work closely with Program Management and Leadership to refine and execute the Institute’s mission and milestones aligning with our strategic goals. They will also lead a diverse team of subject matter experts, including computational biologists, quantitative and modeling scientists, and software engineers, working together to build frameworks that not only mirror real cellular dynamics, but also predict the outcomes of experiments not yet conducted.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Responsibilities:

Leadership and Strategy:

• Provide strategic direction for explanatory modeling efforts, ensuring alignment with the Institute research goals
• Stay at the forefront of emerging advancements in explanatory modeling including agent-based and biophysical continuum modeling and simulations to inform research directions
• Foster a collaborative, cross-disciplinary team environment that encourages creativity, innovation, and integration of diverse modeling approaches
• Work closely with Leadership and Program Management to develop, refine, communicate, and implement the Institute’s strategic vision, ensuring that explanatory modeling contributes meaningfully to broader scientific goals

Research and Development:

• Lead the development of multiscale mechanistic models that explain how cellular events emerge from underlying molecular and biophysical processes, integrating and iterating between agent-based approaches, bottom-up simulations, continuum models, and theory
• Contribute to productive integration of computational and experimental data to build predictive frameworks that can link molecular-scale mechanisms to emergent cellular behaviors observed in imaging data
• Develop a roadmap and proposals for explanatory modeling efforts, identifying key technical risks, dependencies, and milestones in collaboration with Program Management to ensure timely mitigation
• Guide the selection and development of computational tools and methodologies required to scale explanatory modeling approaches, ensuring they align with the Institute’s broader research infrastructure
• Work closely with fellow directors of synthetic biology, quantitative cellular imaging, quantitative image analysis & descriptive modeling, software engineering, and other stakeholders to prioritize, plan and implement explanatory modeling strategies that complement other experimental image-based assay efforts

Management and Mentorship:

• Lead and mentor managers and individuals on a multidisciplinary team of computational biologists, quantitative and modeling scientists, and software engineers, fostering a collaborative environment that integrates diverse expertise
• Scientifically supervise scientists/subject matter experts, as appropriate, for their specific projects
• Oversee the recruitment, training, and career development of team members, supporting their professional growth in computational modeling, mechanistic simulation, and interdisciplinary collaboration
• Foster a culture of learning and knowledge sharing, encouraging team members to stay engaged with cutting-edge developments, other efforts in the institute, and to contribute to the broader research community
• Provide structured performance feedback and mentorship, guiding both early-career and senior scientists toward leadership roles in explanatory modeling

Dissemination and Collaboration:

• Actively participate in scientific conferences and workshops, presenting research findings and networking with the research community
• Establish and maintain collaborations with external researchers and institutions
• Communicate explanatory modeling insights to experimental biologists and other stakeholders, ensuring that these approaches effectively inform hypothesis generation and experimental design
• Advocate for open science and reproducibility, contributing to community-driven initiatives that promote standardized data formats, model sharing, and transparent research practices
• Support external collaboration across disciplines, ensuring that model development is well-integrated with experimental biology, imaging technologies, and data science efforts

*Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

• PhD degree in biological science (e.g., cell biology, developmental biology, biophysics, bioengineering), physical science, or related science, engineering or related field or equivalent combination of degree and experience required
• Established as an expert in explanatory modeling in cell biology with a track record of peer-reviewed publications and/or code repositories demonstrating contributions to mechanistic, agent-based, or multiscale modeling of cellular systems
• Minimum 7 years of professional, post-PhD experience developing and applying computational models to understand cellular behaviors
• Proven leadership qualities with at least 3 years of independent supervisory experience (such as in a laboratory head/PI role)

Preferred Education and Experience

• Minimum 10 years of professional, post-degree experience in explanatory modeling
• Extensive experience with mechanistic, agent-based, or multiscale simulations of cellular systems
• Extensive experience with continuum models in the cellular biophysics space
• Extensive experience in integrating explanatory models with experimental data, particularly in live-cell imaging, single-cell analysis, and/or biophysical measurements
• Proven ability to develop scalable modeling frameworks that link molecular-scale interactions to emergent multicellular behaviors
• Experience in model validation and reproducibility, including the use of community standards for data sharing, metadata annotation, and simulation reproducibility
• Background in developing or applying computational tools for 3D and 4D live-cell image-based analysis and mechanistic simulations
• Experience working in dynamic, fast-paced research environments with a start-up and growth mindset
• Strong collaboration skills, including working with program managers and diverse subject matter experts
• Proven ability to manage projects and people at multiple levels within a multidisciplinary team
• Extensive experience in manuscript writing and collaborative grant writing
• Excellent organizational, written, and verbal communication skills, with strong interpersonal skills for cross-team coordination

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type / Expected Hours of Work

• This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Travel

• Attendance and participation in national and international conferences required

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $206,450 - $270,900 *

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities

Salary : $206,450 - $270,900