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. This position bridges two complementary research efforts within CCB, offering the opportunity to work at the intersection of AI/ML genomic modeling and mechanistic biophysical modeling. Applicants with strong backgrounds in applied and computational mathematics, biophysics, AI/machine learning, computational biology, computer science/engineering, statistical inference, or related fields are encouraged to apply.
CCB has a twofold mission: to develop the rigorous modeling tools and theory needed for understanding biological processes, and to create computational frameworks that will facilitate the analysis of the large, complex data sets being generated by quantitative experimental technologies. To accomplish this, CCB brings together experts in various biological domains (including genomics, molecular, cellular, and developmental biology) whose approaches are informed by the modern computational tools of applied mathematics, statistical inference, artificial intelligence/machine learning (AI/ML), biophysics, and computer science. The goal: to enable CCB to undertake ambitious, long-term research projects that transcend conventional disciplinary boundaries and that lead to a quantitative and predictive understanding of biological phenomena; and to develop high-quality, well-tested, versatile and extensible software across its research areas.
CCB currently comprises more than 50 scientists at career stages from Ph.Ds through senior scientists, as well as visiting scientists and guest researchers, affiliated graduate students and interns. Together, the CCB scientific staff are pioneering an approach to biology in which theory,computation, and experimentation are integrated, from problem conceptualization onwards. This approach enables CCB to tackle not only recognized, fundamental problems in biology that have so far eluded solution, but also, because of the value placed on curiosity-driven research, to find and develop new areas of biological inquiry.
Led by Michael Shelley, the Biophysical Modeling group studies the dynamics of complex and active materials, as well as aspects of collective behavior and self-organization in both natural and synthetic systems. With a focus on complex biophysical systems that arise in cell biology, the group’s research areas include the assembly, structure, positioning and transport of cellular organelles such as the spindle, the organization and dynamics of the nucleus, biophysical fluid-structure problems, and related self-organizing active matter systems.
Led by Olga Troyanskaya, 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.
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.
Reporting to the Group Lead, 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:
Fellows will be based, and have a principal office or workspace, at the Simons Foundation’s offices in New York City. The initial appointments for Flatiron Research Fellows are generally for two years, with the possibility of renewal for a third year, contingent on performance. FRFs may be eligible for subsidized housing within walking distance of CCB.
The anticipated start date is September 2027.
The full-time annual compensation for this position is USD $95,000. In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.
To apply, please submit the following via the application portal:
Applications will generally be reviewed beginning November 2026, and will be considered on a rolling basis until the positions are filled. For full consideration, candidates are strongly encouraged to submit their complete application by November 30, 2026.
Applications will be evaluated based on:
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.
The Flatiron Institute values authenticity, originality, and transparency throughout the application and hiring process. Applicants are expected to submit application materials that reflect their own original work, experiences, ideas, writing, and scientific or professional judgment. The use of AI-based tools may be appropriate for limited purposes during the hiring process, such as editing, formatting, or code review. However, application materials, including research statements, cover letters, personal statements, and other writing samples, should not be substantially authored or generated by AI systems.
Applicants are encouraged to disclose any significant or material use of AI tools in the preparation of their application materials or throughout the hiring process. The Flatiron Institute does not use AI-based tools to screen applicants.
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
The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.
Since its founding in 1994 by Jim and Marilyn Simons, the foundation has been a champion of basic science through grant funding, support for research and public engagement. We believe in asking big questions and providing sustained support to researchers working to unravel the mysteries of the universe.
The Simons Foundation makes grants in four areas: Mathematics & Physical Sciences, Life Sciences, Autism & Neuroscience, and Science, Society & Culture.
Our Flatiron Institute was opened in 2016 and conducts scientific research in-house, supporting teams of top computational scientists.
