Flatiron Research Fellow, Biophysical Modeling & Genomics, CCB

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.

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 AL/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.

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.

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 include but are not limited to:

• Performing theoretical and computational research
• Developing, implementing and maintaining scientific software
• Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars,…