- 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.