Careers

The Simons Foundation’s Flatiron Institute seeks a full-time Research Fellow position as part of its new initiative, Polymathic AI, Building Foundation Models for Science. Recent advances in machine learning, including Large Language Models and diffusion-based generative models have driven significant advances in Artificial Intelligence. The Flatiron Institute seeks to leverage these ideas to develop the next generation of AI-powered scientific analysis tools, seeking more powerful and more interpretable models with broad applications to many scientific disciplines. Our group includes researchers from multiple scientific disciplines ranging from machine learning, to astrophysics, biology, neuroscience, and quantum computing.

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.

Applications are invited for scientists at all levels of seniority at the Center for Computational Mathematics (CCM), in the Flatiron Institute, in all our active areas of research. These include:

● Machine learning, especially the areas of optimization, learning theory, probabilistic modeling, deep learning, and high dimensional data analysis, as well as applications of scientific interest at Flatiron (e.g., cosmological modeling, quantum many-body systems, computational neuroscience)
● Statistical methodology, modeling, and inference
● Probabilistic and differential programming
● Computational physics, including statistical mechanics, biophysics, fluid mechanics, quantum physics, and molecular dynamics
● Numerical methods for partial differential equations and integral equations
● Signal and image processing, with a particular focus on structural biology
● Numerical analysis, including numerical linear algebra and high-order methods
● High performance computing and open source software libraries

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 Flatiron Institute, an internal research division of the Simons Foundation, is a community of scientists who are working to use modern computational tools to advance our understanding of science both through the analysis of large, rich datasets and through the simulations of physical processes. Our mission is to advance scientific research through computational methods, including data analysis, theory, modeling and simulation.

Directed by Dr. Leslie Greengard, the mission at the Flatiron Institute’s Center for Computational Mathematics is to create new mathematical approaches, algorithms and software to advance scientific research in multiple disciplines, often in collaboration with other Flatiron Centers. CCM has particularly strong research groups in the areas of numerical analysis, image and signal processing, computational statistics, and machine learning.

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 Quantum Physics hires seasonal, full-time research interns interested in developing and implementing the concepts, algorithms and codes needed to understand the quantum mechanical behavior of many-particle systems, and to translate this understanding into useful predictions of the behavior of molecules and materials. Under the mentorship of one or more CCQ scientists during the summer, Research Assistants/Associates will contribute to CCQ research by joining an ongoing research project.
 
These are paid, temporary full-time positions based onsite at the foundation here in New York City. Applications are accepted from December 1st until mid-January for the upcoming summer.

Applications are invited to apply for a joint position at the CUNY Graduate Center and the Flatiron Institute’s Center for Computational Neuroscience (CCN). This position is a CUNY faculty position combined with a Visiting Scholar appointment at Flatiron; the visiting scholar position comes with 50% teaching relief at CUNY and access to Flatiron resources as described below.
 
Applicants should have a strong background in the development and use of computational methods in neuroscience. While applicants interested in any of the fields of research supported at CCN will be considered, preference will be given to scientists whose research interests combine computational methods with a systems approach to neuroscience.

The Center for Computational Quantum Physics (CCQ) of the Simons Foundation’s Flatiron Institute, invites applications for temporary full-time positions as Predoctoral Researchers. This program provides graduate students pursuing their PhD in a relevant field the opportunity to be employed at the CCQ for four months for the purpose of working on a research project with one or more CCQ staff mentors. This position will be based onsite at the foundation in New York City. Applicants for this position must have the approval of their thesis advisor. Applications must be submitted by March 30, 2026 for full consideration for the fall 2026 session.

The Initiative for Computational Catalysis (ICC) seeks temporary full-time Pre-doctoral Researchers as part of its Pre-Doctoral Program. This program provides graduate students pursuing their PhD in a relevant field the opportunity to be employed at the ICC for 4 months for the purpose of working on a research project with one or more ICC staff mentors. This position will be based onsite at the foundation in New York City.
 
Applicants for this position should indicate in their application one or more potential mentors at ICC and must have the approval of their thesis advisor. Pre-doctoral sessions will be held in the Fall and Spring. Applications submitted by May 29, 2026 will be considered for the Fall 2026 session. Applications submitted by August 28, 2026 will be considered for the Spring 2027 session.

The Center for Computational Astrophysics (CCA) at the Flatiron Institute, a division of the Simons Foundation, is seeking a full-time research software engineer to develop, maintain, and contribute to the community-oriented software instrument tool MESA (Modules for Experiments in Stellar Astrophysics), and contribute to projects that align with the research directions of the CCA. More information about the CCA can be found on the CCA website. We expect the position to adapt over time to the needs of the broader astronomical community and CCA research community.
 
Research in astronomy and astrophysics depends critically on open source and other scientific software projects that are largely community driven (i.e. not developed or maintained by specific institutions). The primary role of this position (approximately 60% of effort) is to help support the community-oriented software instrument tool MESA.

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.