The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute aims 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.
The Center for Computational Biology (CCB) invites applications for our Summer Research Assistant (undergraduate-level interns), Summer Research Associate (graduate-level interns) and Summer Pre-Doctoral Researcher (2 years of PhD-level studies, started thesis and actively working PIs) internship position(s).
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 Research Scientists, Data Scientists or the Center Director, as appropriate, 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.Learn More
CCB seeks a full-time Associate Research Scientist to develop and design new tools using computer vision to enable new discoveries in biology, and, more broadly, computational science. Areas of current interest include fluorescence reconstruction and image restoration for multi-channel microscopy, self-supervised age estimation using temporal data, and pose estimation for molecular structures in cryo-electron microscopy. However, we are looking for someone who will both collaborate with current work but also pursue their own creative research ideas.
We are seeking an Associate Research Scientist with experience in image processing, computer vision, and deep learning research. The ideal candidate will:
• Enable CCB biologists and biophysicists to denoise, segment, track, and model biological processes using microscopy
• Utilize the latest techniques in computer vision for biology such as self-supervised and contrastive learning, continuous estimation, super-resolution and interpretability
• Collaborate with the other Flatiron Institute centers such as computational neuroscience, computational mathematics and computational astrophysics to utilize state-of-the art computer vision methods to extract information from images
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 and Molecular Biophysics group. The Structural and Molecular Biophysics team, a collaborative effort between CCB and the Center for Computational Mathematics (CCM) uses computational tools to study biological macromolecules, running long timescale molecular simulations and developing statistical analysis and machine learning tools to better capture the dynamics of these molecules and understand their biological function. Areas of interest include in particular statistical mechanics, membrane protein structural biology, protein modeling with flexibility, cryo-electron microscopy, thermodynamics, modeling the effect of mutations, and intrinsically disordered proteins. Applicants with backgrounds in mathematics, statistics, structural biology, computational chemistry, biochemistry, biophysics, or computer science are especially encouraged to apply. We are further interested in those with backgrounds in software development with skills related to methods development in cryo-EM or molecular dynamics simulation or machine learning in the context of computer vision and 3D reconstruction.Learn More
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 Developmental Dynamics group. 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. Itstheoretical and computational work is designed to integrate and abstract rapidly accumulating heterogeneous datasets, to propose critical tests of multiscale regulatory mechanisms, and to guide our own genetic and imaging experiments. 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. Our theoretical and computational work is designed to integrate and abstract rapidly accumulating heterogeneous datasets, to propose critical tests of multiscale regulatory mechanisms, and to guide our own genetic and imaging experiments. Current areas of interest include small cell clusters, graph dynamics in rearranging cell networks, and the effects of activating mutations in signaling enzymes.Learn More
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 Genomics group. 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 data analysis and integration with phenotypic and clinical data; and machine learning 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 (e.g. understanding transcriptional and posttranscriptional regulation and cell type definition) and biomedical (e.g. regulatory variant impact in mental health disorders or cancer). Applicants with backgrounds in machine learning/computer science, biomedical informatics, statistics, applied mathematics, and quantitative biology are especially encouraged.Learn More
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 Group. 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. To address these, often in close collaboration with experimental collaborators, we build numerical and theoretical models from the ground up, revealing how the known mechanics of individual components give rise to collective behavior. Many such phenomena occur only within dense, highly interacting systems, inaccessible to standard techniques. To probe such regimes requires the development of fast and scalable algorithms for many-component systems, and of coarse-grained models that can be analyzed and simulated. Strong applicants with backgrounds in applied and computational mathematics, biophysics, engineering, statistical inference, and related fields are particularly encouraged to apply.Learn More
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 new Biological Transport Networks group. The Biophysical Flow and Networks group, headed by Eleni Katifori, focuses on understanding fluid flows in living organisms. Of particular interest is the modeling of vascular networks across multiple scales, including their function, development and remodeling. We employ advanced computational and theoretical techniques, such as large scale flow network simulations, machine learning, and methods from topological data analysis, to a broad set of problems. Examples include modeling vertebrate and invertebrate circulatory systems, quantifying large datasets of the microvasculature, and understanding and incorporating the effects of nonlinearities into networks of vessels. Applicants with interests in complex networks and biofluid dynamics are particularly encouraged to apply.Learn More