Develop software for reconstruction of biochemical networks spanning multiple
Develop techniques for quantitative prediction and validation of transcript
abundance in an integrated model of metabolism, macromolecular synthesis and
regulation in Geobacter spp.
Develop lifting techniques to enable analysis of multiscale models of biological
Develop quad-precision solvers for linear and quadratic programming, primal-dual
convex optimization and unconstrained dual entropy optimization.
Develop software tools for fundamental operations such as rank-estimation,
basis repair, and null-space computation in stoichiometric analysis.
Design and analyze algorithms for convex optimization problems that arise in analysis and reconstruction of biological networks.
Conduct gradient-based search of kinetic parameters in multiscale models.
Design algorithms for estimation of reaction kinetic parameters from non-stationary
isotopic labeling experiments.