Algorithms

Model specification, simulation and visualization for BioNetGen.

 

Modeling

Uncertain model structure, parallel tempering for parameter optimization, parameter ensemble analysis, Bayesian model selection.

 

Systems

Receptor aggregation (EGFR), endocytosis (EGFR), receptor-mediated signaling (ErbB family, FcεRI receptor, T-cell receptor, EGFR-MAPK-Akt), autophagy (MTORC), transcriptional regulation (Foxp3).

 

Programming

Perl, MatLab, Python, R, BioNetGen (bionetgen.org), rule-based modeling (github.com/RuleWorld/), object-oriented programming.

 

Courses 

Graduate Statistics, machine learning, genomics, molecular evolution, computational structural biology, cell & systems modeling (focus on chemical kinetics).

Undergraduate Protein structure and function, cell biology and signaling, biophysical and biochemical experimental methods.

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