Click here for Krishna's Google Scholar page.


  1. Euler, C., & Mahadevan, R. (2022). On the design principles of metabolic flux sensing.  Biophysical Journal. Click here for the article.
  2. Raj, K., Wong, W. T., Zhang, B., & Mahadevan, R. (2022). Model guided design of enhanced bi-stable controllers to effectively switch cellular states. bioRxiv. Click here for the article.
  3. Liu, Y., & Mahadevan, R. (2022). Genetic engineering of Acidithiobacillus ferridurans with CRISPR-Cas9/dCas9 systems. bioRxiv. Click here for the article.
  4. Xu, Z., Wu, J., Song, Y. S., & Mahadevan, R. (2022). Enzyme activity prediction of sequence variants on novel substrates using improved substrate encodings and convolutional pooling. In Machine Learning in Computational Biology. PMLR. Click here for the article.
  5. Diep, P., Cadavid, J. L., Yakunin, A. F., McGuigan, A. P., & Mahadevan, R. (2022). REVOLVER: a low-cost automated protein purifier based on parallel preparative gravity column workflows. HardwareX. Click here for the article.


  1. Venkatesan, K., Venayak, N., Diep, P., Golla, S. A., Yakunin, A., & Mahadevan, R. (2021). Automation Assisted Anaerobic Phenotyping For Metabolic Engineering. Microbial Cell Factories. Click here for the article.
  2. Diep, P., Boucinha, A., Kell, B., Yeung, B. R. A., Chen, X., Tsyplenkov, D., ... & Ingalls, B. (2021). Advancing undergraduate synthetic biology education: insights from a Canadian iGEM student perspective. Canadian Journal of Microbiology. Click here for the article.
  3. Zhu, L., Pei, W., DiCiano, P., Brands, B., Wickens, C. M., Le Foll, B., ... & Mahadevan, R. (2021). Physiologically-based pharmacokinetic model for predicting blood and tissue tetrahydrocannabinol concentrations. Computers & Chemical Engineering . Click here for the article.
  4. Zhu, L., Pei, W., Thiele, I., & Mahadevan, R. (2021). Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism. PLoS Computational Biology . Click here for the article.
  5. Schneider, P., Mahadevan, R., & Klamt, S. (2021). Systematizing the different notions of growth‐coupled product synthesis and a single framework for computing corresponding strain designs. Biotechnology journal. Click here for the article.
  6. Giannari, D., Ho, C., Mahadevan, R. (2021). A gap filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Computational Biology. Click here for the article.
  7. Hart, K., An, S., Edwards, A. M., Mahadevan, R., Master, E. R., Edwards, E. A. (2021). Could Open Science stimulate industry partnerships in Chemical Engineering university research? Canadian Journal of Chemical Engineering. Click here for the article.
  8. Stephens, S., Mahadevan, R., Allen, G. (2021). Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review. Frontiers in Bioengineering and Biotechnology. Click here for the article.
  9. Pandit, A., Harrison, E., Mahadevan, R. (2021). Engineering Escherichia coli for the utilization of ethylene glycol. Microbial Cell Factories . Click here for the article.
  10. Chen, J., Liu, Y., Diep, P., Mahadevan, R. (2021). Genomic analysis of a newly isolated Acidithiobacillus ferridurans JAGS strain reveals its genetic adaptation to acidic metal-rich environments. Minerals. Click here for the article.
  11. Liu, Y., Benitez, M.G., Chen, J., Harrison, E., Khusnutdinova, A., Mahadevan, R. (2021). Opportunities and challenges for microbial synthesis of fatty acid derived chemicals. Frontiers in Bioengineering and Biotechnology. Click here for the article.


  1. Biz, A., & Mahadevan, R. (2020). Overcoming Challenges in Expressing Iron–Sulfur Enzymes in Yeast. Trends in Biotechnology. Click here for the article.
  2. Davenport-Huyer, L., Mandla, S., Wang, Y., et al. Macrophage Immunomodulation Through New Polymers that Recapitulate Functional Effects of Itaconate as a Power House of Innate Immunity. Adv. Funct. Mater. 2020, 2003341. Click here for the article.
  3. Klamt, S., Mahadevan, R., & Kamp, A. V. (2020). Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. BMC Bioinformatics, 21(1). Click here for the article.
  4. Raj, K., Venayak, N., & Mahadevan, R. (2020). Novel two-stage processes for optimal chemical production in microbes. Metabolic Engineering, 62, 186-197. Click here for the article.
  5. Diep, P., Mahadevan, R., & Yakunin, A. F. (2020). A microplate screen to estimate metal-binding affinities of metalloproteins. Analytical Biochemistry, 609, 113836. Click here for the article.
  6. Correia, K., & Mahadevan, R. (2020). Pan‐Genome‐Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models. Biotechnology Journal, 15(10). Click here for the article.
  7. Liu, Y., Chen, J., Khusnutdinova, A.N., et al. A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. Biotechnol. Biofuels 13(114). (2020). Click here for the article.
  8. Choudhary, R. & Mahadevan, R. Toward a systematic design of smart probiotics. Curr. Opin. Biotech. 64. (2020). Click here for the article.
  9. Liu, Y., Chen, J., Crisante, D., Lopez, J.M.J., Mahadevan, R., Dynamic cell programming with quorum sensing-controlled CRISPRi circuit. ACS Synthetic Biology. 9(6). (2020). Click here for the article.
  10. Al-Fahad, A.J., Al-Fageeh, M.B., Kharbatia, N.M., Sioud, S. & Mahadevan, R., Metabolically engineered recombinant Saccharomyces cerevisiae for the production of 2-Deoxy-scyllo-inosose (2-DOI). Metab. Eng. Commun. 11. (2020). Click here for the article.
  11. Toroghi, M.K., Cluett, W.R., & Mahadevan, R. A personalized multiscale modeling framework for dose selection in precision medicine, Ind. Eng. Chem. Res., 59(21). (2020). Click here for the article.
  12. Chen, J., Liu, A., Diep, P., Jo, A., Nesbø, C., Edwards, E., Papangelakis, P. & Mahadevan, R. Complete genome sequence of Acidithiobacillus ferridurans JAGS isolated from acidic mine drainage, Microbiol. Resour. Announc., 9 (13). (2020). Click here for the article.
  13. Lieven, C., Beber, M.E., Olivier, B.G. et al. MEMOTE for standardized genome-scale metabolic model testing. Nat. Biotechnol. 38272–276. (2020). Click here for the article.
  14. Kim, T., Stogios, P. J., Khusnutdinova, A. N., Nemr, K., Skarina, T., Flick, R., Joo, J. C., Mahadevan, R., Savchenko, A., & Yakunin, A. F. Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol.  J. Biol. Chem., 295(2). (2020). Click here for the article.


  1. Venayak, N., Raj, K. & Mahadevan, R. Impact framework: A python package for writing data analysis workflows to interpret microbial physiology. Metab. Eng. Commun. 9, (2019). Click here for the article.
  2. Srinivasan, S., Cluett, W. R. & Mahadevan, R. A scalable method for parameter identification in kinetic models of metabolism using steady-state data. Bioinformatics (2019). Click here for the article.
  3. Toroghi, M. K., Cluett, W. R. & Mahadevan, R. A multi-scale model for low-density lipoprotein cholesterol (LDL-C) regulation in the human body: Application to quantitative systems pharmacology. Comput. Chem. Eng. (2019). doi:10.1016/j.compchemeng.2019.06.032. Click here for the article.
  4. Correia, K., Yu, S. M. & Mahadevan, R. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution, Database, (2019). Click here for the article.
  5. Wang, P. H. et al. An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME J. (2019). Click here for the article.
  6. Biz, A., Proulx, S., Xu, Z., Siddartha, K., Mulet Indrayanti, A. & Mahadevan, R. Systems biology based metabolic engineering for non-natural chemicals. Biotechnology Adv. (2019). Click here for the article.


  1. Venayak, N., von Kamp, A., Klamt, S. & Mahadevan, R. MoVE identifies metabolic valves to switch between phenotypic states. Nat. Commun. 9, 5332 (2018). Click here for the article.
  2. Venayak, N., Raj, K., Jaydeep, R. & Mahadevan, R. An Optimized Bistable Metabolic Switch to Decouple Phenotypic States during Anaerobic Fermentation. ACS Synth. Biol. 7, 2854–2866 (2018). Click here for the article.
  3. Balderas-Hernández, V. E., Correia, K. & Mahadevan, R. Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid. J. Ind. Microbiol. Biotechnol. (2018). Click here for the article.
  4. Diep, P., Mahadevan, R. & Yakunin, A. F. Heavy metal removal by bioaccumulation using genetically engineered microorganisms. Frontiers in Bioengineering and Biotechnology (2018). Click here for the article.
  5. Nemr, K., Müller, J. E., Joo, J. C., Gawand, P., Choudhary, R., Mendonca, B., Lu, S., Yu, X., Yakunin, A. F. & Mahadevan, R. (2018). Engineering a short, aldolase-based pathway for ( R )-1,3-butanediol production in Escherichia coli. Metabolic Engineering, 48, 13-24. doi:10.1016/j.ymben.2018.04.013. Click here for the article.
  6. Balderas-Hernández, V. E., Correia, K., & Mahadevan, R. (2018). Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: Acetic, formic and levulinic acid. J. Ind. Microbiol. Biot. Click here for the article.
  7. Wang, P., Khusnutdinova, A. N., Luo, F., Xiao, J., Nemr, K., Flick, R., Brown, G., Mahadevan, R., Edwards, E. A. & Yakunin, A. F. (2018). Biosynthesis and Activity of Prenylated FMN Cofactors. Cell Chemical Biology, 25(5). Click here for the article.
  8. Raj, K., Partow, S., Correia, K., Khusnutdinova, A. N., Yakunin A. F. & Mahadevan, R. (2018). Biocatalytic production of adipic acid from glucose using engineered Saccharomyces cerevisiaeMetabolic Engineering Communications. Click here for the article.


  1. Srinivasan, S., Cluett, W. R., & Mahadevan, R. (2017). Model-based design of bistable cell factories for metabolic engineering. Bioinformatics. doi:10.1093/bioinformatics/btx769. Click here for the article. Click here for the associated files.
  2. Klamt, S., Mahadevan, R. and Hädicke, O. (2017), When Do Two-Stage Processes Outperform One-Stage Processes?, Biotechnology Journal, 1700539. doi:10.1002/biot.201700539. Click here.
  3. Garg, S., Judd, K., Mahadevan, R., Edwards, E., & Papangelakis, V. G. (2017). Leaching characteristics of nickeliferous pyrrhotite tailings from the Sudbury, Ontario area. Canadian Metallurgical Quarterly, 56(4), 372-381. doi:10.1080/00084433.2017.1361162. Click here.
  4. Partow, S., Hyland, P. B., & Mahadevan, R. (2017). Synthetic rescue couples NADPH generation to metabolite overproduction in Saccharomyces cerevisiae. Metabolic Engineering, 43, 64-70. doi:10.1016/j.ymben.2017.08.004. Click here.
  5. Khusnutdinova, A. N., Flick, R., Popovic, A., Brown, G., Tchigvintsev, A., Nocek, B., Correia, K., Joo, J. C., Mahadevan, R. and Yakunin, A. F. (2017), Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids. Biotechnology Journal, 12:11, 1600751. doi:10.1002/biot.201600751. Click here.
  6. S. Klamt, G. Regensburger, M.P. Gerstl, C. Jungreuthmayer, S. Schuster, R. Mahadevan, J.Zanghellini, S. Müller, From elementary flux modes to elementary flux vectors: metabolic network and pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology, 13 (2017). Click here.
  7. Kim T, Flick R, Brunzelle J, Singer A, Evdokimova E, Brown G, Joo JC, Minasov GA, Anderson WF, Mahadevan R, Savchenko A, Yakunin AF. 2017. Novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol: structural and biochemical studies. Applied Environmental Microbiology 83:e03172-16. Click here.
  8. Wang, P., Tang, S., Nemr, K., Flick, R., Yan, J., Mahadevan, R., Yakunin, A.F., Loffler, F.E., Edwards, E. A. (2016). Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. The ISME Journal11(3), 626-640. doi:10.1038/ismej.2016.158. Click here.
  9. Garg, S., Papangelakis, V., Edwards, E., Mahadevan, R., (2017). Application of a selective dissolution protocol to quantify the terminal dissolution extents of pyrrhotite and pentlandite from pyrrhotite tailings. International Journal of Mineral Processing, 158, 27-34. Click here.
  10. Pandit AV, Srinivasan S, Mahadevan R. Redesigning metabolism based on orthogonality principles. Nature Communications 2017;8:15188. doi:10.1038/ncomms15188. Click here.
  11. J.C. Joo, et al. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chemical Sciences, 8 (2016), pp. 1406-1413. Click here.


  1. Toroghi M. K., Cluett W. R. , Mahadevan R. Multiscale Metabolic Modeling Approach for Predicting Blood Alcohol Concentration. IEEE Life Sciences Letters 2016 2(4): 59-62. Click here.
  2. Rodenhizer D, Gaude E, Cojocari D, et al. A 3D engineered tumour for spatial snap-shot analysis of cell metabolism and phenotype in hypoxic gradients. Nature Materials 2016 ;15(2):227-234. doi:10.1038/nmat4482. Click here.
  3. Islam, M. A., Tchigvintsev, A., Yim, V., Savchenko, A., Yakunin, A. F., Mahadevan, R. and Edwards, E. A. (2016), Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. Microbial Biotechnology , 9: 47–60. doi:10.1111/1751-7915.12315. Click here.


  1. Ebrahim A., Almaas E., Bauer E., Bordbar A., Burgard A. P., Chang R. L., et al. . (2015). '? Molecular Systems Biology 11, 831. 10.15252/msb.20156157. Click here.
  2. S. Srinivasan, W. R. Cluett and R. Mahadevan, “Constructing kinetic models of metaboli sm at genome-scales: A review”, Biotechnology Journal. 2015, 10(9):1345-59. Click here.
  3. N. Venayak, N. Anesiadis, W. R. Cluett, and R. Mahadevan, “Synthetic Biology Tools for Dynamic Control of Metabolism”, Current Opinion in Biotechnology, 2015, 34C:142-152. Click here.
  4. Klamt, R. Mahadevan, On the feasibility of growth-coupled product synthesis in microbial strains, 2015, Metabolic Engineering 30: 166-178. Click here.
  5. Nicholas Gold; Christopher M Gowen; Francois-Xavier Lussier; Sarat C Cautha; Radhakrishnan Mahadevan; “Vincent Martin, Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics”, 2015, Microbial Cell Factories 14(73). Click here.
  6. R. Mahadevan, A. von Kamp, S. Klamt; Genome-scale strain designs based on regulatory minimal cut sets, Bioinformatics, Volume 31, Issue 17, 1 September 2015, Pages 2844–2851. Click here.
  7. 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.
  8. P. Gawand, F. Said-Akbar, N. Venayak, S. Partow, A. E. Motter, R. Mahadevan, “Sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions”, 2015, Integrative Biology, 7(8):930-9. Click here.
  9. A. Islam, E. A. Edwards, K. Zengler, R. Mahadevan, and G. Stephanopoulos, “Investigating Moorella thermoacetica Metabolism with a Genome-Scale Constraint-Based Metabolic Model”, 2015, Integrative Biology, 7(8):869-82. Click here.


  1. Jayasinghe, N., Franks, A., Nevin, K. P. and Mahadevan, R. (2014), Metabolic modeling of spatial heterogeneity of biofilms in microbial fuel cells reveals substrate limitations in electrical current generation. Biotechnology Journal, 9: 1350–1361. doi:10.1002/biot.201400068. Click here.
  2. Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R, New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PLoS One. 2014 Apr 14;9(4):e94808. doi: 10.1371. Click here.
  3. Gawand, P., Mahadevan R., Engineering Escherichia coli for D-ribose production from glucose-xylose mixtures. Industrial Biotechnology, 2014, 10(2): 106-114. Click here.
  4. Bourdakos N, Marsili E, Mahadevan R. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell. 2014, Biotechnology and Bioengineering. 2014 Apr;111(4):709-18. doi: 10.1002. Click here.


  1. Gawand P, Hyland P, Ekins A, Martin VJ, Mahadevan R. Novel approach to engineer strains for simultaneous sugar utilization. 2013, Metabolic Engineering 20, 63-72. Click here.
  2. Salimi, F., R. Mahadevan, “Characterizing Metabolic Interactions in a Clostridial Co-culture for Consolidated Bioprocessing”, 2013, BMC Biotechnology, 13(1), 95. Click here.
  3. Zhao, J., Scheibe, T. and Mahadevan R. Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation. Chemical Geology, 2013, 357, 215-222. Click here.
  4. G. D. Tartakovsky, A. M. Tartakovsky, T. D. Scheibe,Y. Fang, R. Mahadevan, D. R. Lovley, Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport. 2013, Advances in Water Resources, 59, 256-270. Click here.
  5. P. Hyland, S. M. Lock, R. Mahadevan, “Prediction of Weak Acid Toxicity in Saccharomyces cerevisiae using Genome Scale Metabolic Models”, 2013, Industrial Biotechnology,9 (4), 229-235. Click here.
  6. Zheng H, Beliavsky A, Tchigvintsev A, Brunzelle JS, Brown G, Flick R, Evdokimova E, Wawrzak Z, Mahadevan R, Anderson WF, Savchenko A, Yakunin AF, “Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium.”, 2013, Proteins, 81(6):1031-41. Click here.
  7. N. Anesiadis, H.Kobayashi, W. R. Cluett, R. Mahadevan, “Analysis and design of a genetic circuit for dynamic metabolic engineering”, 2013, ACS Synthetic Biology,2(8):442-52. Click here.
  8. K. Zhuang, L. Yang, W. Cluett, R. Mahadevan, “Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design". 2013, BMC Biotechnology,13:8. Click here.
  9. S. Javaherian, N. Anesiadis, R. Mahadevan, A. McGuigan, “Design principles for generating robust gene expression patterns in dynamic engineered tissues”, 2013, Integrative Biology,5(3):578-89. Click here.


  1. R. Mahadevan, and M. Henson, “Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities”, 2012, Computational and Structural Biotechnology Journal, 3:4. Click here.
  2. Zhuang, K., Ma, E., Lovley, D. R. and Mahadevan, R. (2012), The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnology & Bioengineering., 109: 2475–2483. doi:10.1002/bit.24528 Click here.
  3. Suzuki, H., MacDonald, J., Khajamhoidddin, S., Salamov A., Hori C., Aerts, A., Henrissat, B., Wiebenga, A., Barry, K., Lindquist, E., Labutti, K., Lapidus, A., Lucas, S., Coutinho, P., Gong, Y., Samejima, M., Mahadevan R., Abou-Zaid, M., de Vries, R., Igarashi, K., Yadav, J., Grigoriev, I., and E. R. Master, “ Comparative genomics of the white rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. 2012, 13:444, BMC Genomics. Click here.
  4. Facchini, P., J. Bohlmann, P.S. Covello, V. De Luca, R. Mahadevan, J.E. Page, D.-K. Ro, C.W. Sensen. R. Storms, and V.J.J. Martin. Synthetic biosystems for the production of high-value plant metabolites. 2012, 30(3), 127-131. Trends in Biotechnology. Click here.
  5. Barlett, M., Zhuang, K., Mahadevan, R., and Lovley, D.: Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation, Biogeosciences, 9, 1033-1040,, 2012. Click here.
  6. Khazaei T, McGuigan A, Mahadevan R. "Ensemble Modeling of Cancer Metabolism". Frontiers in Physiology. 2012;3:135. doi:10.3389/fphys.2012.00135. Click here.


  1. D. Pinel. P. Gawand, R. Mahadevan, V. Martin, “‘Omics’ technologies and systems biology for engineering Saccharomyces cerevisiae strains for lignocellulosic bioethanol production". 2012, 30(3), 127-131. Biofuels. Click here.
  2. A. V. Pandit and R. Mahadevan, “An in silico Characterization of  Microbial Electrosynthesis for Metabolic Engineering of Biochemicals”. Microbial Cell Factories, 2011, 10:76. Click here.
  3. J. Usher, V. Balderas, A. Johnston, P. Quon, N. Gold, V. Martin, L. Harris, R. Mahadevan and K. Baetz, “Chemical and synthetic genetic array analysis identifies genes that suppress xylose utilization and fermentation in Saccharomyces cerevisiae. 2011,1, 247:258, G3 : Genes, Genomes, Genetics. Click here.
  4. 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.
  5. K. Zhuang, G. Vemuri, R. Mahadevan, "Economics of Membrane Occupancy and the Respiro-fermentation,” Molecular Systems Biology, 2011, 7:500. Click here.
  6. J. Zhao, and R. Mahadevan, “Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation affecting uranium bioremediation”, Biotechnology and Bioengineering, 2011, 108(7):1537-1548. Click here.
  7. Y. Fang, T. D. Scheibe, R. Mahadevan, S. Garg, P. E. Long, and D. R. Lovley, “Direct Coupling of a Genome-Scale Microbial in silico model and a groundwater reactive transport model”, Journal of Contaminant Hydrology, 2011, 122(1-4):96-103. Click here.
  8. R. Mahadevan, B. Palsson, and D. Lovley, “In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale  modeling”, Nature Reviews Microbiology, 2011, 9(1), 39-50. Click here.

2010 and Before

  1. Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2010). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME Journal, 5(2), 305-316. doi:10.1038/ismej.2010.117. Click here.
  2. A. Islam, E. Edwards, and R. Mahadevan, “Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model”, PLoS Computational Biology, 2010,6(8). Click here.
  3. 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.
  4. S. Garg, L. Yang, and R. Mahadevan, “Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling”, BMC Research Notes, 2010, 3:125. Click here.
  5. K. Srinivasan, R. Mahadevan, “Characterization of Proton Production and Consumption Associated with Microbial Metabolism”, BMC Biotechnology , 2010, 10:2. Click here.
  6. J. Zhao, T.D. Scheibe, Y. Fang, D.R. Lovley, R. Mahadevan, “ Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments”, Journal of Contaminant Hydrology, 2010, 112(1-4):30-44. Click here.
  7. C. Risso, J. Sun, K. Zhuang, R. Mahadevan, D. R. Lovley et al., “ Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens . ”, BMC Genomics, 2009, 10:447. Click here.
  8. T.D. Scheibe, R. Mahadevan, Y. Fang, S. Garg, P. Long, and D.R. Lovley, “ Coupling a Genome-scale Metabolic Model with a Reactive Transport Model to describe in situ uranium bioremediation. ”, Microbial Biotechnology, 2009, 2(2):274-86. Click here.
  9. J. Sun, B. Sayyar, J.E. Butler, P. Pharkya, T.R.Fahland,I. Famili, C.H. Schilling, D.R. Lovley, and R. Mahadevan, “ Genome-scale constraint-based modeling of Geobacter metallireducens ”, BMC Systems Biology, 2009, 3:15. Click here.
  10. N. Anesiadis, W. R. Cluett, and R. Mahadevan, “ Dynamic Metabolic Engineering for Increasing Bioprocess Productivity”, Metabolic Engineering, 2008,10(5):255-66. Click here.
  11. M. Izallalen, R. Mahadevan, A. Burgard, B. Postier, R. didonato Jr., J. Sun, C. H. Schilling, and D. R. Lovley, “ Geobacter sulfurreducens Strain Engineered for Increased Rates of Respiration”, Metabolic Engineering, 2008, 10(5):267-75. Click here.
  12. L. Yang, W. R. Cluett and R. Mahadevan, “A Bilevel Optimization Algorithm to Identify Enzymatic Capacity Constraints in Metabolic Networks”, Computers and Chemical Engineering,2008, 32(9):2072-2085. Click here.
  13. P. Dhurjati and R. Mahadevan, “ Systems Biology: A Synergistic Interplay Between Biology and Mathematics”, Canadian Journal of Chemical Engineering, 2008,86(2):127-141. Click here.
  14. R. Mahadevan, B. Yan, B. Postier, K. P. Nevin, T. L. Woodard, R. O Neil, M. Coppi, B. Methe, J. Krushkal, “ Characterizing Regulation of Metabolism in Geobacter sulfurreducens through Genome-wide Expression Data and Sequence Analysis”, Omics, 2008,12(1):33-59. Click here.
  15. R. Mahadevan and D. R. Lovley, “The Degree of Redundancy in Metabolic Genes Is Linked to Mode of Metabolism”, Biophysical Journal, 2008, 94(4):1216-20. Click here.
  16. D. Segura, D. R. Lovley, and R. Mahadevan, “Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens”, PLoS Computational Biology, 2008, 4(1):e36. Click here.
  17. Y.K. Oh, S. M. Park, B.O. Palsson, C. H. Schilling and R. Mahadevan, “Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data”, Journal of Biological Chemistry, 2007, 282(39):28791-9. Click here.
  18. J. L. Hjersted, R. Mahadevan, and M. A. Henson,“Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture”, Biotechnology and Bioengineering, 2007, 97 (5), 1190-204. Click here.
  19. K. G. Gadkar, R. Mahadevan, and F. J. Doyle III, “Batch Control of Genetic Alterations for Optimal Metabolic Engineering”, Automatica, 2006, Oct; 42(10), 1723-1733. Click here.
  20. R. Mahadevan, C. H. Schilling, D. R. Bond, D. R. Lovley, “Characterization of metabolism in the Fe (III)-reducing organism Geobacter sulfurreducens by constraint-based modeling”, Applied and Environmental Microbiology, 2006, 72(2), 1558-1568. Click here.
  21. R. Mahadevan, A. P. Burgard, I. Famili, S. Van Dien, and C. H. Schilling, “Applications of Metabolic Modeling to drive Bioprocess Development for the production of Value-Added Chemicals”, Biotechnology and Bioprocess Engineering, 2005, 10:408-417. Click here.
  22. I. Famili, R. Mahadevan, and B. O. Palsson, “k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network-scale”, Biophysical Journal, 2005, 88(3), 1616-25. Click here.
  23. R. Mahadevan, and B. O. Palsson, “Properties of Large-Scale Biochemical Networks: Structure vs. Function”, Biophysical Journal, 2005, 88(1), L07-L09. Click here.
  24. K. G. Gadkar, F. J Doyle III, J. S. Edwards, and R. Mahadevan, “Estimating optimal profiles of genetic alterations using constraint‐based models”, Biotechnology and Bioengineering, 2005, 89(2), 243-251. Click here.
  25. S. J. Wiback, R. Mahadevan, and B. O. Palsson, “Using Metabolic Flux Data to Further Constrain the Metabolic Solution Space and Predict Internal Flux Patterns: The Escherichia coli -Spectrum”, Biotechnology and Bioengineering, 2004, 86(3), 317-331. Click here.
  26. R. Mahadevan, C. H. Schilling, “ Effects of Alternate Optimal Solutions in Constraint-based Genome Scale Metabolic Models”, Metabolic Engineering, 2003, 5:264-276. Click here.
  27. S. J. Wiback, R. Mahadevan, and B. O. Palsson, “Reconstructing metabolic flux vectors from extreme pathways: defining the α-spectrum”, Journal of Theoretical Biology, 2003, 224:313-324. Click here.
  28. R. Mahadevan and F. J. Doyle III, “On-line Optimization of a Recombinant Product in a Fed-batch Bioreactor ”, Biotechnology Progress, 2003, 19(2), 639-646. Click here.
  29. R. Mahadevan and F. J. Doyle III, “Efficient Optimization Approaches to Nonlinear Model Predictive Control”, International Journal of Robust and Nonlinear Control, 2003, 13 (3-4): 309-329. Click here.
  30. R. Mahadevan, J. S. Edwards, and F. J. Doyle III, “Dynamic Flux Balance Analysis Approaches”, Biophysical Journal, 2002, 83, 1331-1340. Click here.
  31. R. Mahadevan, A. C. Allcock, and F. J. Doyle III, “Control-relevant Scheduling of Polymer Grade Transitions”, AIChE Journal, 2002, 48(8), 1754-1764. Click here.
  32. Mahadevan R., Agrawal S. K., and Doyle III F. J., “Differential Flatness based Nonlinear Predictive Control of Fed-batch Bioreactors”, Control Engineering Practice, 2001, 9(8), 889-899. Click here.