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Job Title

Postdoctoral Fellow – Computational Modeling, Simulation, and Inference in Biological Systems

Workplace

The Agmon Lab (https://vivariumlab.com/), part of the Center for Cell Analysis and Modeling at UConn Health, develops computational frameworks for building, composing, and analyzing multiscale biological simulations. We develop and maintain Vivarium, an open-source modular simulation framework, and apply it to biological systems ranging from microbial physiology and whole-cell modeling to microbial communities, tissue-scale systems, and other complex biological processes. Our work combines mechanistic modeling, numerical simulation, probabilistic inference, and software infrastructure to build predictive models that can integrate diverse biological data and

generate testable hypotheses. We collaborate broadly across computational biology, systems biology, bioinformatics, microbial physiology, and multicellular modeling.

Project Description

This postdoctoral position will contribute to the development of general computational approaches for simulating and inferring the behavior of complex biological systems. Current areas of interest include microbial physiology, whole-cell modeling, microbial communities, multiscale tissue models, and compositional frameworks for integrating heterogeneous biological models and datasets.

The position will emphasize simulation-based inference, numerical modeling, uncertainty-aware prediction, and the development of scalable computational workflows. Depending on the candidate’s interests and background, projects may involve high-throughput simulation of E. coli model variants, inference of missing gene functions, integration of large-scale experimental datasets, development of modular simulation infrastructure, or extension of these approaches to microbial communities and multicellular/tissue systems.The postdoc will have opportunities to collaborate with leading experimental and computational groups, contribute to open-source modeling infrastructure, and help shape a research program at the intersection of biological theory, simulation, and data-driven inference.

Job Description

We seek a highly motivated Postdoctoral Researcher with strong quantitative and computational skills. The ideal candidate will have a background in computational biology, applied mathematics, statistics, physics, computer science, systems biology, or a related field, and an interest in using models to understand biological systems. The role will involve developing and analyzing computational models, designing simulation and inference workflows, working with biological datasets, and contributing to reusable software tools. A strong candidate will be comfortable thinking mathematically, programming carefully, and engaging deeply with biological questions.

Requirements

• PhD in Computational Biology, Systems Biology, Bioinformatics, Applied Mathematics, Statistics, Physics, Computer Science, or a related field.
• Strong programming skills, preferably in Python.
• Experience with numerical simulation, computational modeling, statistical inference, machine learning, optimization, or data analysis.
• Interest in biological modeling, including microbial systems, cellular systems, multicellular systems, or multiscale modeling.
• Ability to work independently while collaborating effectively with interdisciplinary teams.
• Strong communication skills and interest in publishing scientific findings and open-source tools.
• Experience with any of the following is a plus: systems biology models, agent-based modeling, probabilistic programming, Bayesian inference, high-performance computing, bioinformatics databases, genome-scale modeling, whole-cell modeling, or scientific software development.

Responsibilities

• Develop computational models and simulation workflows for complex biological systems.
• Apply numerical, statistical, and inference-based methods to analyze model behavior and biological datasets.
• Contribute to open-source simulation infrastructure, including Vivarium and related tools.
• Collaborate with experimental and computational research teams to integrate data and validate model predictions.
• Publish results in peer-reviewed journals and present findings at conferences.
• Help shape new research directions in simulation-based biological discovery.

Benefits

• Competitive salary with comprehensive medical and dental insurance.
• Access to advanced computational resources and a highly collaborative research environment.
• Opportunity to contribute to open-source infrastructure for biological modeling.
• Flexibility to develop projects aligned with the candidate’s quantitative strengths and biological interests.
• Supportive, inclusive lab environment with strong emphasis on mentorship and career development.

Availability

• This position is available with a starting date in Summer/Fall 2026. For further details or to apply, please contact Dr. Eran Agmon at agmon@uchc.edu.