Multiscale Systems Biology Collaboration

Papers

• Y. Sun, R. M. T. Fleming, M. A. Saunders, and I. Thiele, Robust flux balance analysis of multiscale biochemical reaction networks, BMC Systems Biology, in revision, May 2013.

• J. D. Lee, Y. Sun, and M. A. Saunders, Proximal Newton-type methods for minimizing composite functions, Report SOL 2013-1, 27 pp.
  Preliminary version:

  • J. D. Lee, Y. Sun, and M. A. Saunders, Proximal Newton-type methods for minimizing composite functions, Advances in Neural Information Processing Systems 25, 2012.

• S. Akle, O. Dalal, R. M. T. Fleming, M. A. Saunders, N. A. Taheri, and Y. Ye, Existence of positive steady states for mass conserving and mass-action chemical reaction networks with a single terminal-linkage class, arXiv:1106:2359.

• I. Thiele, R. M. T. Fleming, R. Que, A. Bordbar, and B. O. Palsson, Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage, PLoS One 7(9):e45635 (2012).

• J. Nogales, S. Gudmundsson, E. M. Knight, B. O. Palsson, and I. Thiele, Systems biology of photosynthesis in cyanobacteria: detailing network optimality properties, submitted.

• J. A. Lerman, D. R. Hyduke, H. Latif, V. A. Portnoy, N. E. Lewis, J. D. Orth, A. C. Schrimpe-Rutledge, R. D. Smith, J. N. Adkins, K. A. Zengler, and B. O. Palsson, Quantitative genome-scale simulation of molecular biology and metabolism, submitted.

• R. M. T. Fleming, C. M. Maes, M. A. Saunders, Y. Ye, and B. O. Palsson, A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks, J. Theor. Biol. 292 (2012), pp. 71–77.

• See also UCSD Systems Biology Research Group publications.

Talks

• M. A. Saunders, I. Thiele, R. M. T. Fleming, B. O. Palsson, Y. Ye, S. Akle, O. A. Dalal, J. A. Lerman, Y. Sun, and N. A. Taheri, Satisfying flux balance and mass-action kinetics in a network of biochemical reactions, DOE Genomic Science Awardee Meeting IX, Crystal City, VA, Apr 10–13, 2011.

• S. Akle, O. A. Dalal, R. M. T. Fleming, M. A. Saunders, N. A. Taheri, and Y. Ye, Existence of positive equilibria for mass conserving and mass-action biochemical reaction networks with a single terminal-linkage class, DOE Genomic Science Awardee Meeting IX, Crystal City, VA, Apr 10–13, 2011.

• R. M. T. Fleming, Stoichiometric modelling of biochemistry: A variational approach, Biomedical Engineering Department seminar, University of Texas at Dallas, Mar 11, 2011.

• R. M. T. Fleming, On optimality principles in nonequilibrium biochemical networks, 11th International Conference on Systems Biology, Edinburgh, Oct 2010.

• I. Thiele, Expanding genome-scale metabolic models, Workshop IOMPA, 11th International Conference on Systems Biology, Edinburgh, Oct 2010.

• R. M. T. Fleming, A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks, Para 2010: State of the Art in Scientific and Parallel Computing in Reykjavik, Jun 2010.