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Flatiron Research Fellow, Center for Computational Biology

Simons Foundation
New York, New York, United States
Closing date
Nov 3, 2022

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Life Sciences, Biology, Other Life Science
Organization Type
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POSITION SUMMARY The Center for Computational Biology (CCB) of the Simons Foundation's Flatiron Institute invites applications for multiple post-doctoral Flatiron Research Fellows (FRF) positions. Applications will be reviewed beginning in Fall 2022, and considered on a rolling basis until the positions are filled. For full consideration, submission of a complete application by November 15, 2022 is strongly recommended 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. - CCB welcomes applicants interested and capable in the following areas of research: * Biological Transport Networks: Areas of interest include modeling of vascular networks at multiple scales, including their function, development and remodeling, using machine learning and methods from topological data analysis to quantify large datasets of the microvasculature, understanding and incorporating the effects of fluid structure interactions (e.g. valves) into large scale networks of vessels. Applicants with interests in fluid dynamics and applied mathematics, networks or machine learning are particularly encouraged to apply. * Biophysical Modeling: Areas of interest include the dynamics of complex and active materials, and collective behavior and self-assembly in both natural systems (e.g., inside the cell) and synthetic ones. Approaches are based on mathematical modeling and analysis, the development and application of software tools for large-scale biophysical simulation, and close collaboration with experimentalists. Applicants with backgrounds in computational and applied mathematics, and theoretical biophysics are especially encouraged. * Developmental Dynamics: Areas of interest include small cell clusters, graph dynamics in rearranging cell networks, and the effects of activating mutations in signaling enzymes. 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. * Genomics: 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. * Structural and Molecular Biophysics: Areas of interest include developing and using mathematical approaches and computational algorithms to understand the molecular mechanisms involved in key biological processes using cryo-electron microscopy experiments. * Structural Biology: Areas of interest include in particular membrane protein structural biology, protein modeling with flexibility, structure prediction, protein-protein interactions, high-resolution refinement, protein design, modeling the effect of mutations, and the integration of experimental data. We are further interested in analyzing sequence-structure-function relationships of large-scale microbiome databases and integrating structural methods with machine learning algorithms. FRFs 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. - 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, workshops and meetings * Participating in the preparation of manuscripts for publication and of presentations at scientific conferences * Assisting in student mentorship * Sharing expertise and providing training and guidance to CCB staff and visitors as needed. FRF positions are generally two-year appointments that can be renewed for a third year, contingent on performance. Fellows will be based, and have a principal office or workspace, at the Simons Foundation's offices in New York City. Fellows may also be eligible for subsidized housing within walking distance of the Flatiron Institute. MINIMUM QUALIFICATIONS Education * Ph.D. in a relevant field Related Skills & Other Requirements * Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis * Ability to do original and outstanding research in computational biology, and expertise in computational methods, data analysis, software and algorithm development, modeling machine learning, and scientific simulation * Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists * Strong oral and written communication, data documentation, and presentation skills REQUIRED APPLICATION MATERIALS * Cover Letter, which should include a summary of applicants' most significant contributions in graduate school * Curriculum vitae with publications list and, if relevant, links to software * Research statement of no more than three (3) pages describing the applicant's past important results, current and future research interests which may include both scientific topics and algorithm and software development, and potential synergies with activities at CCB * Two (2) letters of recommendation submitted confidentially by the recommenders directly to DEADLINE Applications for available positions that begin in 2023 will generally be reviewed beginning mid-November 2022, 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 11, 2022. More information about career opportunities at the Simons Foundation's Flatiron Institute is also available at THE SIMONS FOUNDATION'S DIVERSITY COMMITMENT Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law. PI193528283

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