Click here for Krishna's Google Scholar page.
2022
- Euler, C., & Mahadevan, R. (2022). On the design principles of metabolic flux sensing. Biophysical Journal. Click here for the article.
- 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.
- Liu, Y., & Mahadevan, R. (2022). Genetic engineering of Acidithiobacillus ferridurans with CRISPR-Cas9/dCas9 systems. bioRxiv. Click here for the article.
- 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.
- 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.
2021
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Pandit, A., Harrison, E., Mahadevan, R. (2021). Engineering Escherichia coli for the utilization of ethylene glycol. Microbial Cell Factories . Click here for the article.
- 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.
- 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.
2020
- Biz, A., & Mahadevan, R. (2020). Overcoming Challenges in Expressing Iron–Sulfur Enzymes in Yeast. Trends in Biotechnology. Click here for the article.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Choudhary, R. & Mahadevan, R. Toward a systematic design of smart probiotics. Curr. Opin. Biotech. 64. (2020). Click here for the article.
- 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.
- 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.
- 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.
- 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.
- Lieven, C., Beber, M.E., Olivier, B.G. et al. MEMOTE for standardized genome-scale metabolic model testing. Nat. Biotechnol. 38, 272–276. (2020). Click here for the article.
- 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.
2019
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
2018
- 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.
- 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.
- 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.
- 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.
- 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.
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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.
- 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.
- 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 cerevisiae. Metabolic Engineering Communications. Click here for the article.
2017
- 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.
- 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.
- 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.
- 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.
- 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.
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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.
- 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.
- 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 Journal, 11(3), 626-640. doi:10.1038/ismej.2016.158. Click here.
- 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.
- Pandit AV, Srinivasan S, Mahadevan R. Redesigning metabolism based on orthogonality principles. Nature Communications 2017;8:15188. doi:10.1038/ncomms15188. Click here.
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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.
2016
- 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.
- 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.
- 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.
2015
- 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.
- 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.
- 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.
- Klamt, R. Mahadevan, On the feasibility of growth-coupled product synthesis in microbial strains, 2015, Metabolic Engineering 30: 166-178. Click here.
- 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.
- 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.
- 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.
- 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.
- 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.
2014
- 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.
- 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.
- Gawand, P., Mahadevan R., Engineering Escherichia coli for D-ribose production from glucose-xylose mixtures. Industrial Biotechnology, 2014, 10(2): 106-114. Click here.
- 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.
2013
- 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.
- Salimi, F., R. Mahadevan, “Characterizing Metabolic Interactions in a Clostridial Co-culture for Consolidated Bioprocessing”, 2013, BMC Biotechnology, 13(1), 95. Click here.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
2012
- 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.
- 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.
- 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.
- 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.
- 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, https://doi.org/10.5194/bg-9-1033-2012, 2012. Click here.
- 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.
2011
- 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.
- 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.
- 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.
- 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.
- K. Zhuang, G. Vemuri, R. Mahadevan, "Economics of Membrane Occupancy and the Respiro-fermentation,” Molecular Systems Biology, 2011, 7:500. Click here.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- K. Srinivasan, R. Mahadevan, “Characterization of Proton Production and Consumption Associated with Microbial Metabolism”, BMC Biotechnology , 2010, 10:2. Click here.
- 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.
- 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.
- 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.
- 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.
- N. Anesiadis, W. R. Cluett, and R. Mahadevan, “ Dynamic Metabolic Engineering for Increasing Bioprocess Productivity”, Metabolic Engineering, 2008,10(5):255-66. Click here.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- R. Mahadevan, and B. O. Palsson, “Properties of Large-Scale Biochemical Networks: Structure vs. Function”, Biophysical Journal, 2005, 88(1), L07-L09. Click here.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- R. Mahadevan, J. S. Edwards, and F. J. Doyle III, “Dynamic Flux Balance Analysis Approaches”, Biophysical Journal, 2002, 83, 1331-1340. Click here.
- 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.
- 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.