Journals & Proceedings

Refereed Journal Articles (71) & Conference Proceedings (18)

89) Nazanin Samadifard, Cheryl E. Devine, Elizabeth Edwards, Radhakrishnan Mahadevan, and Vladimiros G. Papangelakis*, Ferric sulphate leaching of pyrrhotite tailings. Minerals, 2015, Accepted

88) Rodenhizer, E. Gaude, D. Cojocari, R. Mahadevan, C. Frezza, B. G .Wouters, A.P. McGuigan.TRACER: a 3D engineered tumour for mapping cell metabolism and phenotype in heterogeneous microenvironments. Accepted, Nature Materials, 2015.

87) Ebrahim et al., Do Genome-scale Models Need Exact Solvers or Clearer Standards ? 2015, Accepted, Molecular Systems Biology.

86) Islam, A. Savchenko, A. Yakunin, R. Mahadevan, E. Edwards, Experimental Validation of In Silico Model-Predicted Isocitrate dehydrogenase and Phosphomannose isomerase from Dehalococcoides mccartyi Strain KB-1. 2015, Accepted, Microbial Biotechnology.

85) Klamt, R. Mahadevan, On the feasibility of growth-coupled product synthesis in microbial strains, 2015, Accepted, Metabolic Engineering.

84) Gawand, F. Said-Akbar, N. Venayak, S. Partow, A. E. Motter, R. Mahadevan, “The sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions”, 2015, Integrative Biology, 7(8):930-9.

83) 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.

82) 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, Accepted.

81) Mahadevan*, A. Von Kamp, S. Klamt, “Genome-scale strain designs based on regulatory minimal cut sets”, 2015, Bioinformatics, Accepted.

80) S. Srinivasan, W. R. Cluett and R. Mahadevan*, “Towards constructing genome-scale kinetic models of metabolism”, Biotechnology Journal. 2015, 10(9):1345-59.

79) 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.

78) 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.

77) N. Jayasinghe, A. Franks, C. Xu, K. Nevin, T. Russell, D. Lovley, and R. Mahadevan*, “Metabolic Modeling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells”. Biotechnology Journal, 2014, Accepted.

76) Gawand, P., Mahadevan R., Engineering Escherichia coli for D-ribose production from glucose-xylose mixtures. Industrial Biotechnology, 2014, 10(2): 106-114.

75) 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.

74) Bourdakos N, Marsili E, Mahadevan R A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell. 2014, Biotechnol Bioeng.2014 Apr;111(4):709-18. doi: 10.1002.

73) Salimi, F., R. Mahadevan, “Characterizing Metabolic Interactions in a Clostridial Co-culture for Consolidated Bioprocessing”, 2013, BMC Biotechnology, 13(1), 95.

72) Gawand P, Hyland P, Ekins A, Martin VJ, Mahadevan R. Novel approach to engineer strains for simultaneous sugar utilization. 2013, Metab Eng. 20, 63-72.

71) 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.

70) 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.

69) 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.

68) 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.

67) 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.

66) K. Zhuang, L. Yang, W. Cluett, R. Mahadevan, “DyScO: Dynamic Scanning and Optimization for Integrated Strain and Bioprocess Development. 2013, BMC Biotechnology,13:8.

65) 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.

64) R. Mahadevan, and M. Henson, “Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities”, 2012, Computational and Structural Biotechnology Journal, 3.

63) 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.

62) S. Chautha, V. Martin, F. X Lussier, N. Gold, C. Gowen, R. Mahadevan, “Ensemble Modeling of S. cerevisiae for Tyrosine Production”, 2013, Computer Applications in Biotechnology, Mumbai.

61) K. Zhuang, E. Ma, R. Mahadevan, “Optimization of Bioremediation Strategy using Genome-scale Dynamic Models of Microbial Communities”, In Press, Biotechnology and Bioengineering.

60) S. Garg, V. G. Papangelakis, R. Mahadevan, E. Edwards, E. Krause, “Bioleaching of Pyrrhotite Tailings for Ni Extraction – Is it possible? Proceedings of the 51st Annual Conference of Metallurgists, Niagara Falls, ON, September 30- October 3, 2012.

59) T. Khaezei, A. McGuigan, R. Mahadevan, “Ensemble Modeling of Cancer Metabolism”, Accepted to Frontiers in Computational Physiology and Medicine.

58) M. Barlett*, K. Zhuang, D. Lovley, R. Mahadevan, “Integrative Analysis of the Interactions between Geobacter spp. and Sulfate-Reducing Bacteria during Uranium Bioremediation”, Accepted to Biogeosciences.

57) 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. Trend Biotechnol. (Featured on the Cover Page)

56) A. V. Pandit and R. Mahadevan*, “An in silico Characterization of  Microbial Electrosynthesis for Metabolic Engineering of Biochemicals”.  2011, 10:76. Microbial Cell Factories.

55) D. Pinel. P. Gawand, R. Mahadevan, V. Martin, “High-throughput ‘omics’ technologies and systems biology for developing Saccharomyces cerevisiae strains for lignocellulosic bioethanol production. 2012, 30(3), 127-131. Biofuels.

54) 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.

53) L. Yang, W. R. Cluett, and R. Mahadevan*, “EMILiO: A fast algorithm for genome-scale strain design”. 2011, 13(3):272-281. Metabolic Engineering.

52) K. Zhuang, G. Vemuri, R. Mahadevan, ” Economics of Membrane Occupancy and the Respiro-fermentation,” Nature Group’s Molecular Systems Biology, 2011, 7:500.

51) J. Zhao, and R. Mahadevan*, “Sensitivity Analysis of an Integrated Reactive Transport Model to Identify Factors Critical for Effective Bioremediation”, Biotechnology and Bioengineering, 2011, 108(7):1537-1548.

50) 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.

49) N. Anesiadis, W. R. Cluett, R. Mahadevan, “Model-driven  design based on sensitivity analysis for a synthetic biology application”, Proceedings of the 21st European Symposium on Computer Aided Process Engineering (2011), Chalikidiki, Greece.

48) 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. (Was featured on the cover, see link )

47) A. Islam, E. Edwards, and R. Mahadevan*, “Pan-Genome Scale Metabolic Modeling of Dehalococcoides species”, PLoS Computational Biology, 2010,6(8).

46) K. Zhuang, C. Risso, M. Izallalen, H. Richter, P. Mouser, R. Mahadevan, and D. R. Lovley, “Genome-Scale Dynamic Modeling of Competition among Rhodoferax and Geobacter in anoxic environments”, 2010, Nature Group’s ISME Journal, doi: 10.1038/ismej.2010.117.

45) 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.

44) S. Garg, L. Yang, and R. Mahadevan*, “Analysis of Regulation of Metabolism in G. sulfurreducens using Constraint-based Modeling”, BMC Research Notes, 2010, 3:125

43) K. Srinivasan, R. Mahadevan*, “Characterization of Proton Production and Consumption Associated with Microbial Metabolism”, BMC Biotechnology , 2010, 10:2.

42) J. Zhao, T.D. Scheibe, Y. Fang, D.R. Lovley, R. Mahadevan*, “ Analysis of the Impact of Electron Capacitance on the Extent of Uranium Reduction ”, Journal of Contaminant Hydrology, 2010, 112(1-4):30-44.

41) L. Yang, R. Mahadevan and W. R. Cluett, “Rapid Design of System-wide Metabolic Network Modifications using Iterative Linear Programming”, Proceedings of the 2010 DYCOPS conference, Belgium. (Selected as a Keynote Presentation)

40) N. Jayasinghe, R. Mahadevan, “Metabolic Modeling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells”, Proceedings of the 2010 Conference on Computer Applications in Biotechnology, Belgium.

39) F. Salimi, R. Mandal, D. Wishart, R. Mahadevan, “Understanding Clostridium acetobutylicum ATCC 824 Metabolism Using Genome-Scale Thermodynamics and Metabolomics-based Modeling”, Proceedings of the 2010 Conference on Computer Applications in Biotechnology, Belgium.

38) L. Yang, R. Mahadevan and W. R. Cluett, “Designing Experiments from Noisy Metabolomics Data to Refine Constraint-based Models”, American Control Conference, Boston, U.S.A, 2010. (Selected as the Best Presentation in the Session)

37)  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.

36) 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.

35) 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.

34) K. Zhuang, D. Lovley, R. Mahadevan, “Dynamic Modeling of the Ecology of Desulfovibrio vulgaris, Geobacter sulfurreducens and Acetate Oxidizing Sulfate Reducers”, Proceedings of the 2009 Foundations of Systems Biology in Engineering Conference, Englewood, CO.

33) 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.

32) N. Anesiadis, W. R. Cluett, and R. Mahadevan*, “ Dynamic Metabolic Engineering for Increasing Bioprocess Productivity”, Metabolic Engineering, 2008,10(5):255-66.

31) 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.

30) 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.

29) P. Dhurjati and R. Mahadevan*, “ Systems Biology: A Synergistic Interplay Between Biology and Mathematics”, Canadian Journal of Chemical Engineering, 2008,86(2):127-141.

28) D. Segura, D. R. Lovley, and R. Mahadevan* “Experimental and Computational Analysis of Redundancy in Central Metabolism of Geobacter sulfurreducens”, PLoS Computational Biology, 2008, 4(1):e36.

27) R. Mahadevan* and D. R. Lovley, “Analysis of Degree of Genetic Redundancy in Genome-Scale Bacterial Metabolic Networks”, Biophysical Journal, 2008, 94(4):1216-20.

26) J. Krushkal,M. Puljic, B. Yan, J. F. Barbe, R. Mahadevan, B. Postier, R. A. O’Neil**, G. Reguera, C. Leang, L. N. DiDonato, C. Núñez, B. A. Methé, R. M. Adkins, and D. R. Lovley. Genome regions involved in multiple regulatory pathways identified using GSEL, a genome-wide database of regulatory sequence elements of Geobacter sulfurreducens.IEEE Proceedings, 2008 International Conference on BioMedical Engineering and Informatics (BMEI 2008).

25) Y.K. Oh, S. M. Park, B.O. Palsson, C. H. Schilling and R. Mahadevan*, “Iterative model development of Bacillus subtilis”, Journal of Biological Chemistry, 2007, 282(39):28791-9.

24) 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.

23) J. L. Hjersted, M.A. Henson, and R. Mahadevan, “Validation of a Saccharomyces cerevisiae dynamic flux balance model and analysis of metabolism and ethanol production in fed-batch culture”, Proceedings of the 2007 Foundations of Systems Biology in Engineering Conference, Stuttgart, Germany.

22) 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.

21) R. Mahadevan*, C. H. Schilling, D. R. Bond, D. R. Lovley, “Metabolic Model of Geobacter sulfurreducens”, Applied and Environmental Microbiology, 2006, 72(2), 1558-1568.

20) R. Mahadevan, A. Esteve-Nunez, D.R. Bond, and D. R. Lovley, “Constraint-based modeling of the Fe(III) reducing bacteria, Geobacter sulfurreducens, Proceedings of the 2006 Systems Biology Conference, Madrid, Spain.

19) 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.

18) 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.

17) R. Mahadevan*, and B. O. Palsson, “Properties of Large-Scale Biochemical Networks: Structure vs. Function”, Biophysical Journal, 2005, 88(1), L07-L09.

16) K. G. Gadkar, F. J Doyle III, J. S. Edwards, and R. Mahadevan*, “Design of Optimal Genetic Manipulation Strategies for Metabolic Engineering”, Biotechnology and Bioengineering, 2005, 89(2), 243-251.

15) K. G. Gadkar, R. Mahadevan, F. J. Doyle III, “Batch control of genetic alterations for optimal metabolic engineering”, American Control Conference, 2005, Portland, U.S.A.

14) 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.

13) R. Mahadevan and F. J. Doyle III, “Partial Flatness based Approach to Nonlinear Moving Horizon Estimation”, American Control Conference, Boston, U.S.A, 2004.

12) R. Mahadevan*, C. H. Schilling, “ Effects of Alternate Optimal Solutions in Constraint-based Genome Scale Metabolic Models”, Metabolic Engineering, 2003, 5:264-276.

11) S. J. Wiback, R. Mahadevan, and B. O. Palsson, “Decomposing Steady State Flux Vectors into Extreme Pathways: Defining the alpha-Spectrum”, Journal of Theoretical Biology, 2003, 224:313-324.

10) R. Mahadevan and F. J. Doyle III, “Efficient On-line Optimization of a Recombinant Product in a Fed-batch Bioreactor ”, Biotechnology Progress, 2003, 19(2), 639-646.

9) 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.

8 ) R. Mahadevan, J. S. Edwards, and F. J. Doyle III, “Dynamic Flux Balance Analysis Approaches”, Biophysical Journal, 2002, 83, 1331-1340.

7) R. Mahadevan, A. C. Allcock, and F. J. Doyle III, “Control-relevant Scheduling of Polymer Grade Transitions”, AIChE Journal, 2002, 48(8), 1754-1764.

6) K. Pathak, R. Mahadevan and S. K. Agrawal, “Model Reformulation Schemes in Dynamic Optimization: A Numerical Study of the Flexible Link”, Proceedings of NATO-ASI Workshop on Virtual Nonlinear Multibody systems, Prague, Czech Republic, 2002.

5) R. Mahadevan, S. K. Agrawal, and F. J. Doyle III, “Differential Flatness based Nonlinear Predictive Control of Fed-batch Bioreactors”, Control Engineering Practice, 2001, 9(8), 889-899.

4) R. Mahadevan and F. J. Doyle III, “Optimization of a Fed-batch Bioreactor based on State Transformations”, Topical Conference on Bioinformatics and Genomics at the AIChE Annual Meeting, Reno, NV, November 2001.

3) F. J. Doyle III, K. Troutman, E. S. Meadows, E. P. Gatzke, R. Vadigepalli, R. Mahadevan, G. Whitmyre, G. Stoole, and P. Richards, “Innovative Control Education Using a 4-Tank Experiment and the WWW”, IFAC/IEEE Symposium on Advances in Control Education, Gold Coast, Australia, December 2000.

2) R. Mahadevan, S. K. Agrawal, and F. J. Doyle III, “Flatness based Approach to Optimization of Fed-batch Bioreactors”, IFAC Symposium on Advanced Control of Chemical Processes, Pisa, Italy, 2000, 111-116.

1) R. Mahadevan and F. J. Doyle III, “Nonlinear Nonsquare Control of a Continuous Bioreactor using Flat Outputs”, European Control Conference, Karlsruhe, Germany, 1999, 416-422.

*: Corresponding Author