Summer Research Interns, Center for Computational Biology

The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute invites applications to its 2026 summer internship program. 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.

ABOUT CCB

The mission of the Center for Computational Biology is to develop rigorous modeling tools and theory for understanding biological processes, and to create computational frameworks that will enable the analysis of the large, complex data sets being generated by novel and increasingly quantitative experimental technologies. CCB’s research activities span scales of biological organization, from phenomena unfolding at the atomistic and molecular level to those observed at the cell, tissue and organismal level. 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.

POSITION SUMMARY

For Summer 2026, CCB is recruiting interns across all research groups: 

Biological Transport & Networks: CCB's research on biological transports and networks aims to unravel the intricate relationships between the architecture of biological transport networks, their physical and developmental constraints, and their contribution to the overall fitness of the organisms they serve. The work seeks to integrate computation, theory, and experimental data to bridge micro- and mesoscopic knowledge of living processes and networks. Summer interns will be working on vascular topopolgy and function (via the development of computational models aimed at elucidating the relationship between morphology and function in mammalian vasculature) and the development of transport-informed models of neuronal growth.

Biomolecular Design: The Biomolecular Design team applies theory and builds computational tools for robust and rational design of protein or protein-like heteropolymers for making new drugs or self-organizing biomaterials, or to catalyze previously inaccessible catalytic reactions. Summer 2026 interns may work on designing cyclic peptoid foldamer macrocycles to bind target proteins for live cell imaging by CCBScope, and developing protocols for the rapid sampling of intrinsically disordered protein (IDP) conformational ensembles using Monte Carlo methods.

Biophysical Modeling: The Biophysical Modeling group focuses on the modeling and simulation of complex systems that arise in biology and soft condensed matter physics. Scientists working in this group develop both theoretical models and the software needed for large-scale dynamics simulation of continuum and many-body physics problems. Potential intern projects for Summer 2026 include (1) developing an improved numerical method for accurate and efficient evaluation of the Bingham closure for polar active suspensions; (2) deriving a reduced-order model by inference techniques instead of analytical methods; and (3) developing a kinetic model of polymer condensation that accounts for interactions among condensates and between condensates and the unclustered polymer chain.

CCBScope: The CCBScope Observatory is an in-house imaging facility where CCB scientists develop and apply quantitative workflows for 3D and long-term time-lapse imaging to resolve dynamics at cellular and subcellular scales. The CCBScope summer intern project combines live imaging, modeling and simulations to elucidate the biophysical mechanisms driving the cytoskeletal-mediated repositioning of the nucleus in the developing egg cell of the fruit fly. Interns will learn how to dissect and prepare biological samples, operate a confocal microscope for live imaging, and use high-performance computing to simulate the transport of a deformable nucleus driven by centrosomes in the realistic geometry of the fly oocyte.

Computer Vision & Machine Learning: CCB's computer vision & machine learning work is propelled by extensive collaboration among CCB scientists from different research areas  to develop new tools for quantifying dynamic processes, from cell divisions during early mammalian development to the packing of tubular structures like spermatozoa during reproduction. Potential projects for summer interns include (1) to develop generalizable strategies for segmentation of small cell clusters by use of transfer learning, leveraging simulated data and other existing annotated ground truth datasets; (2) to develop network architectures for 4D instance segmentation and cell event detection, or (3) to design new approaches for the detection and measurement of elongated tubular biological structures such as microtubules and spermatozoa.

Developmental Dynamics: In the area of developmental dynamics, CCB focuses on the mechanistic modeling of pattern formation and morphogenesis; the synthesis and decomposition of developmental trajectories; and the modeling of human developmental defects. Summer intern projects will include developing mathematical cleavage divisions in mammalian embryos using a combination of theoretical and image processing approaches, as well the development of computational models of small cell clusters, motivated by experimental work on the formation of primordial germs.

Genomics: The Genomics group  works to unravel the complexity of the genome, its regulation, and its phenotypic consequences, through the accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to disease. Summer interns with the Genomics group will have opportunities to contribute to ongoing research in computational genomics and data-driven biology, including the exploration of multimodal single-cell data integration, deep learning, and other modern machine learning approaches to study gene regulation, human genetics and disease.

Statistical Biophysics: CCB scientists in the statistical biophysics group work on information processing in biological networks and nonequilibrium thermodynamics of living systems. Building on a recent publication, summer interns with the Statistical Biophysics team will use simulations and theory to study the non-equilibrium mechanisms by which bacterial flagellar motors integrate chemical and mechanical signals.

Structural & Molecular Biophysics: CCB’s work on structural & molecular biophysics focuses on developing mathematical approaches to understand the mechanisms at play in the functioning of important biomolecules such as transmembrane proteins.Summer interns will focus on methods development for cryo-EM analysis, likely developing code for better extraction of conformational heterogeneity from raw particle images or improving machine learning methods for pose estimation.

Interns will be assigned a primary mentor and research group within the center, and will participate in research group’s meetings and seminars as well as their own designated project(s). Interns  will also participate in other center- and Flatiron Institute-wide activities such as guest lectures, training on use of the Institute’s robust scientific computing resources, and intern networking activities.

When submitting their application materials, applicants must indicate the group(s) to which they are applying. Applicants may submit applications to multiple groups.

EDUCATION

• Applicants must be currently pursuing or recently completed a bachelor’s, master’s, or be pursuing their PhD program in applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematics physics, or related disciplines. 

RELATED SKILLS & EXPERIENCE

• Demonstrated abilities in mathematical modeling, biophysical 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.


• Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists.


• Strong oral and written communication, data documentation, and presentation skills.


• Excellent collaborative and interpersonal skills.

REQUIRED APPLICATION MATERIALS

Applicants must submit the following: 

• Resume or CV


• Transcript (official or unofficial)


• Cover letter (1 page max, essay and/or bullet points) which addresses the applicant’s interest in computational biology as well as their qualifications and interest in the specific research group(s) to which they are applying.

COMPENSATION

• Interns at the undergradaute level will earn $20/hour.


• Interns at the graduate level will earn $25/hour.


• Interns at the pre-doctoral level (2 years of PhD-level studies, started thesis and actively working with PIs) will earn $28/hour. 

PROGRAM TIMELINE

• December 1, 2025: Application portal opens. 


• January 16, 2026: Application portal closes. 


• February 27, 2026: Offers made, with response due by March 13, 2026. 


• June 1, 2026: Summer internship program begins.


• August 14, 2026: Summer internship program ends. 

Our Commitment to Expanding Pathways to Science & Opportunities for All:

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