Flatiron Research Fellow Biophysical Modeling & Genomics

About the Center for Computational Biology (CCB)

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is actively seeking enthusiastic, full-time post-doctoral Flatiron Research Fellows to join its Biophysical Modeling and Genomics groups in 2026. The goal at CCB is to advance the understanding of fundamental and historically challenging biological processes by developing theory, innovative modeling tools for large-scale biophysical simulations, and computational frameworks for analyzing increasingly large and complex experimental datasets. Living systems are built hierarchically; as such, CCB’s research activities span several scales of biological organization, bridging the gap between microscopic detail and large-scale behaviors, and providing natural continuity between our groups’ efforts. CCB currently comprises more than 45 research and data scientists at career stages from recent Ph.D. graduates through senior scientists, as well as visiting scientists, guest researchers, graduate students, interns, and administrative support staff. For a full description of CCB research areas and scientific staff, please see our website.

Research Focus: Biophysical Modeling and Genomics

This joint position bridges two complementary efforts within CCB. The Biophysical Modeling group focuses on the modeling and simulation of complex systems that arise in biology and soft condensed matter physics. Areas of interest include the dynamics of complex and active materials, and aspects of collective behavior and self-organization in both natural systems (e.g., inside the cell) and synthetic ones. The Genomics group develops AI/ML methods to interpret genomes and distill the immensely complex networks that form the foundation of human biology and disease. Current areas of interest include developing foundation models for genome interpretation; creating methods for multi-omic and spatial data analysis and integration with phenotypic and clinical data; and advancing AI-based frameworks for network modeling and regulatory module detection. Together, these groups aim to develop integrative, hybrid models that combine deep learning for genome interpretation with mechanistic biophysical representations of its structure, dynamics, and regulation. Their joint work seeks to build theoretical and computational frameworks that link genome-scale regulatory models with quantitative, physics-based understanding of molecular and cellular organization. A key focus is on predictive modeling of how genetic variation alters the biophysical properties of neurons and the downstream phenotypic manifestations relevant to ASD and related conditions.

Unique Interdisciplinary Opportunity

The uniqueness of this position lies in its explicitly interdisciplinary nature—offering the opportunity to work at the intersection of AI/ML genomic modeling and mechanistic biophysical modeling—and in its close integration with directed experimental investigations within the CCBx experimental network. Strong applicants with backgrounds in applied and computational mathematics, biophysics, AI/machine learning, computational biology, computer science/engineering, statistical inference, or related fields are particularly encouraged to apply.

POSITION DESCRIPTION

Flatiron Research Fellows in CCB are individuals at the postdoctoral level with backgrounds in one or more of the following areas: applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines. Fellows are expected to carry out an active research program that can be independently directed and/or involve substantial collaboration with other members of CCB or the Flatiron Institute. In addition to their research, Fellows help build the rich scientific community at CCB and the Flatiron Institute by participating in seminars, colloquia, and group meetings; developing their software, mathematical and computational expertise through internal education opportunities; and sharing their knowledge through scientific publications, presentations, and/or software releases, with the financial support of the Institute. Fellows have access to the Flatiron Institute’s powerful scientific computing resources.

Responsibilities

• Performing theoretical and computational research
• Developing, implementing and maintaining scientific software
• Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars, workshops and meetings
• Participating in the preparation of manuscripts for publication and of presentations at scientific conferences
• Assisting in student mentorship
• Sharing expertise and providing training and guidance to CCB staff and visitors as needed.

FRF positions are generally two-year appointments that can be renewed for a third year, contingent on performance. Fellows will be based, and have a principal office or workspace, at the Simons Foundation’s offices in New York City. Fellows may also be eligible for subsidized housing within walking distance of the Flatiron Institute. For more information about careers at the Flatiron Institute, please click here.

Qualifications

Education

Ph.D. in a relevant field (applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines)

Related Skills & Other Requirements

• Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis
• Ability to do original and outstanding research in computational biology, and expertise in computational methods, data analysis, software and algorithm development, modeling machine learning, and scientific simulation
• Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
• Strong oral and written communication, data documentation, and presentation skills

COMPENSATION AND BENEFITS

The full-time annual compensation for this position is $91,000. In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.

Application Instructions

To apply, please submit the following via the application portal:

• Cover Letter, which should include a summary of applicants’ most significant contributions in graduate school
• Curriculum vitae with publications list and, if relevant, links to software
• Research statement of no more than three (3) pages describing the applicant’s past important results, current and future research interests which may include both scientific topics and algorithm and software development, and potential synergies with activities at CCB
• Two (2) letters of recommendation

Applications for available positions that begin in 2025 will generally be reviewed beginning November 2025, and will be considered on a rolling basis until the positions are filled.

SELECTION CRITERIA

Applications will be evaluated based on:

• Past research accomplishments
• The proposed research program
• The synergy of applicant’s expertise and research proposal topic with existing CCA staff and research programs, and potential to cross boundaries between CCB groups and/or the Flatiron Institute’s other research centers.

Any queries about the application process or about CCB should be directed to ccbjobs@flatironinstitute.org. Queries about CCB may also be directed to scientific staff at CCB.

Equal Employment Opportunity Statement

Our Commitment to Expanding Pathways to Science & Opportunities for All: Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds, and experiences. The Simons Foundation is committed to advancing basic science and mathematics to benefit humankind and expand our collective understanding of our world. As part of our mission, we support partners, programs, and initiatives that seek to broaden the scientific community and open pathways to science and mathematics careers. The Simons Foundation provides equal opportunities to all applicants without regard to race, religion, color, age, sex, pregnancy, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state, and local law.

Key skills/competency

• Biophysical Modeling
• Genomics
• AI/ML
• Computational Biology
• Mathematical Modeling
• Scientific Software Development
• Data Analysis
• Statistical Inference
• Interdisciplinary Research
• Postdoctoral Research