Multiscale Systems Biology Collaboration

Workflows for multiscale model reconstruction and systematic validation using transcriptomic data

  • Develop software for reconstruction of biochemical networks spanning multiple cellular subsystems.

  • Develop techniques for quantitative prediction and validation of transcript abundance in an integrated model of metabolism, macromolecular synthesis and regulation in Geobacter spp.

Algorithms for convex optimization in systems biology

  • Develop lifting techniques to enable analysis of multiscale models of biological networks.

  • 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.

Multiscale mass conserved elementary kinetic modeling

  • Conduct gradient-based search of kinetic parameters in multiscale models.

  • Design algorithms for estimation of reaction kinetic parameters from non-stationary isotopic labeling experiments.