Many of our recent tools and downloads can be found in our GitHub page: https://github.com/LMSE
Srinivasan, S., Cluett, W. R., and Mahadevan, R., Model-based Design of Bistable Cell Factories for Metabolic Engineering, Bioinformatics, 2017. Click here for the article. Click here for the code.
L. Yang, S. Srinivasan, W. R. Cluett, and R. Mahadevan,“ Characterizing metabolic pathway diversification in the context of perturbation size”, Metabolic Engineering, 2015, 28,114-22. Click here for the article. EMILiO (MATLAB) zip archive
N. Jayasinghe, A. Franks, K.P. Nevin and R. Mahadevan, Metabolic modeling of spatial heterogeneity of biofilms in microbial fuel cells reveals substrate limitations in electrical current generation. Biotechnology Journal, 2014, 9: 1350–1361. doi:10.1002/biot.201400068. Click here for the article. MATLAB files accompanying the paper in a zip archive.
L. Yang, W. R. Cluett, and R. Mahadevan, “EMILiO: A fast algorithm for genome-scale strain design”. 2011, 13(3):272-281. Metabolic Engineering. Click here for the article. EMILiO (MATLAB) zip archive
K. Zhuang, M. Izallalen, P. Mouser, H. Richter, C. Risso, R. Mahadevan and D.R. Lovely, “Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments”. ISME Journal, 2011 5(2): 305-16. Click here for the article. DyMMM: Dynamic Multispecies Metabolic Modeling framework on SourceForge.
K. Zhuang, G. Vemuri, R. Mahadevan, “Economics of Membrane Occupancy and the Respiro-fermentation,” Molecular Systems Biology, 2011, 7:500. Click here for the article. COBRA Model of E. coli in MATLAB format, SBML format
F. Salimi, K. Zhuang and R. Mahadevan, “Genome-scale Metabolic Modeling of a Clostridial Co-culture for Consolidated Bioprocessing”, Biotechnology Journal, 2010,5(7):726-738. Click here for the article. Clostridium cellulolyticum and Clostridium acetobutylicum models in SBML format.