Careers

The Center for Computational Biology is seeking an experienced software engineer to be the Project Lead for HumanBase (hb.flatironinstitute.org), a dynamic and interactive web-based platform that supports thousands of biomedical researchers in exploring the molecular mechanisms of human disease. This position is ideal for an experienced engineering leader with bioinformatics experience who thrives on solving complex problems at the intersection of large-scale data, advanced analytics, and scientific discovery. This is a high-impact role that directly advances the study of human genomics and disease.

The successful candidate will lead technical direction and execution, guide other software engineers, and collaborate closely with researchers at the Center for Computational Biology to translate cutting-edge computational biology into robust software tools. The Project Lead will be a hands-on engineering leader with experience in biological data and -omics technology, as well as a complementary skillset that includes both writing high-quality code and managing a small team of software engineers. Success in this role depends on the ability to translate biological questions into computational solutions, collaborate closely with internal scientific stakeholders, and drive technically rigorous projects that advance our understanding of human biology.

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is seeking full-time post-doctoral Flatiron Research Fellows to join its Biophysical Modeling group in 2026. 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. Ongoing projects focus on understanding the organization and dynamics of the nucleus, the structure and assembly of spindles, the positioning and transport of cellular organelles, and fluid-structure problems in biology. Strong applicants with backgrounds in applied and computational mathematics, biophysics, engineering, statistical inference, and related fields are particularly encouraged to apply.

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is seeking full-time post-doctoral Flatiron Research Fellows to join its Developmental Dynamics group in 2026. The Developmental Dynamics group combines experiments, theory and computing to elucidate the contributions of encoded genomic instructions and self-organizing physical mechanisms to embryonic development. The group’s research is organized around three main themes: the mechanistic modeling of pattern formation and morphogenesis; the synthesis and decomposition of developmental trajectories; and the modeling of human developmental defects. We are looking for candidates interested in data-driven modeling of biological systems, especially in the context of behavioral changes during postembryonic development. We have devised a throughput approach for recording such changes in Drosophila and are evaluating a range of data analysis and modeling for data mining.

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is seeking full-time post-doctoral Flatiron Research Fellows to work on information processing in biological networks and nonequilibrium thermodynamics of living systems. Current areas of interest include (but not limited to) molecular mechanisms and nonequilibrium thermodynamics in living systems responsible for important regulatory functions such as signal transduction, molecular motor control, synchronization of biochemical oscillations, and gene regulation.

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is seeking full-time post-doctoral Flatiron Research Fellows to join its Biological Transport Networks group in 2026. The primary objective of the Biological Transport Networks group is to unravel the intricate relationships among the architecture of transport networks, their physical and developmental constraints, and their contribution to the overall fitness of the organisms they serve. Ultimately, we seek to integrate computation, theory and experimental data to bridge our micro- and mesoscopic knowledge of living processes and the intricacies of large-scale networks. By doing so, we aspire to unveil biological principles that can provide insights into comparative physiology across different species. Of particular interest is the modeling of transport networks across multiple scales, including their function, development and remodeling.

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 Structural & Molecular Biophysics and Biomolecular Design groups for a joint appointment in 2026, as part of the Collaboration on Molecular Physics and Sampling Strategies (COMPASS). The Structural & Molecular Biophysics group uses long timescale molecular dynamics (MD) simulations, integrated with experimental observables (especially cryo-electron microscopy data), and machine learning tools to better capture the dynamics of biological macromolecules and to understand their function. Complementing this work, the Biomolecular Design group applies the current understanding of the theory of protein folding and function to design new, synthetic heteropolymers, built from exotic chemical building blocks, which fold into new structures inaccessible to natural proteins, and which perform new functions. In addition to giving rise to useful new molecules that can serve as drugs, nanomaterials, or catalysts, this also serves as the ultimate test of our understanding of protein folding.Together through the Molecular Ensemble Sampling and Simulation (MESS) collaboration, the groups are working together to advance computational methods for the design and understanding of molecular motion, and addressing current obstacles to accuracy and tractability. The successful candidate will carry out a research project to advance these goals. Particular foci include 1) engineering open-source software infrastructure to facilitate analysis of macromolecular motion and design of motile macromolecules, 2) integration of physics-based simulation and machine learning methods, 3) development of enhanced approximation methods (implicit solvation, coarse-graining, etc.) to improve the tractability of currently expensive calculations, 4) the incorporation of molecular design tools to interpret cryo-EM data, or 5) the design of molecules of potential medical interest.

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. 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. 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. 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.

Each summer, the Center for Computational Biology hires seasonal, full-time research interns interested in developing modeling tools and theory for understanding biological processes, and in creating computational frameworks to analyze the large, complex data sets being generated by new experimental technologies. The full-time paid internship will run from June 1, 2026 through August 14, 2026 in New York City, with housing and roundtrip travel expense reimbursement for non-local interns. Mentored directly by CCB scientists, summer interns will contribute to ongoing CCB research projects, engage with the broader scientific community with the Flatiron Institute and the Simons Foundation; and actively participate in Summer at Simons programming. For summer 2026, we are recruiting interns for all CCB research groups, including Biological Transport & Networks, Biomolecular Design, Biophysical Modeling, Developmental Dynamics, Genomics, Statistical Biophysics, Computer Vision & Machine Learning and Statistical Biophysics. Applications will be accepted from December 1, 2025 through January 16, 2026.

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is seeking full-time post-doctoral Flatiron Research Fellows to join its Genomics group in 2026. The Genomics group works to interpret genomes and distill the immensely complex networks that form the foundation of human biology and disease, through accurate machine learning models. Current areas of interest include developing deep learning approaches for genome interpretation; development of methods for multi-omic and spatial data analysis and integration with phenotypic and clinical data; and machine learning and AI approaches for network modeling and regulatory module detection. These and other methods are developed in tight collaboration with experimental biologists, biomedical scientists, and clinicians and are applied to specific biological problems, both fundamental and biomedical.