Postdoc: Computational Immunology & Viral Modeling

University of Pittsburgh; Pittsburgh (Allegheny County); On-site; USD 60,000 - 80,000; Full time

Job summary

The Faeder Lab at the University of Pittsburgh seeks a postdoctoral associate to develop mechanistic computational models of immune signaling and viral replication, including EEEV replication and interferon restriction.

The position collaborates with NIH-funded groups in Immunology and with ML partners to integrate models with gene-expression data. You will refine simulations, perform parameter estimation and contribute to methods papers, while mentoring students.

Qualifications

• PhD (or near completion) in computational biology, systems biology, biophysics, physics, applied mathematics, computer science, statistics or a related quantitative field.
• Experience with ODE or stochastic modeling and parameter estimation; familiarity with Bayesian inference, sequential Monte Carlo or nonlinear mixed-effects methods is a strong plus.
• Programming proficiency in Python; experience with scientific computing, performance optimization or compiled languages (for example C++) is an advantage for the simulation methods work.
• Experience with rule-based modeling (BioNetGen, Kappa) or with modeling of intracellular signaling or viral replication is an advantage.
• Ability to work with experimental collaborators and to communicate quantitative results clearly to a mixed computational and experimental audience.
• Strong communication skills and a collaborative, critically engaged working style.

Responsibilities

• Refactor published models into modular representations and recalibrate with new data.
• Extend models to include interferon-mediated restriction mechanisms and identify sensitive steps.
• Perform Bayesian parameter estimation with regularization and uncertainty analyses.
• Develop and analyze identifiable network models of cytokine signaling and JAK–STAT pathways.
• Fit models to single-cell measurements and extend to population-level variability.
• Collaborate with machine learning groups to combine mechanistic models with gene expression predictions.
• Develop, benchmark and optimize simulation algorithms and software for rule-based models.
• Prepare methods manuscripts and document new simulation capabilities.
• Present results at lab meetings and conferences; mentor students as appropriate.

Skills

Python programming

C++ programming

Scientific computing

Performance optimization

Bayesian inference

Monte Carlo methods

Nonlinear mixed-effects

BioNetGen

Kappa

Intracellular signaling modeling

Education

PhD in computational biology or related field

Tools

BioNetGen

Kappa

Job description

The Faeder Lab at the University of Pittsburgh seeks a postdoctoral associate to develop mechanistic computational models of immune signaling and viral replication, including EEEV replication and interferon restriction.

The position collaborates with NIH-funded groups in Immunology and with ML partners to integrate models with gene-expression data. You will refine simulations, perform parameter estimation and contribute to methods papers, while mentoring students.