Research Topics
| Radhakrishnan MahadevanSummaryAffiliation: University of Toronto Country: Canada Publications
| Collaborators
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Detail Information
Publications
Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysisRadhakrishnan Mahadevan
Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
OMICS 12:33-59. 2008..sulfurreducens and simulated Fe(II)-limited growth. The resulting prediction was consistent with data, suggesting that regulatory constraints are important for simulating growth phenotypes in nonoptimal environments...
Genome-scale constraint-based modeling of Geobacter metallireducensJun Sun
Genomatica Inc, San Diego, CA, USA
BMC Syst Biol 3:15. 2009..Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens...- Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducensCarla Risso
Department of Microbiology, 203N Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA
BMC Genomics 10:447. 2009..ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies... - The degree of redundancy in metabolic genes is linked to mode of metabolismR Mahadevan
Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
Biophys J 94:1216-20. 2008..Rather, the degree of gene duplication in microorganisms may be linked to mode of metabolism and environmental niche... - Thermodynamic analysis of regulation in metabolic networks using constraint-based modelingSrinath Garg
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario M5S3E5, Canada
BMC Res Notes 3:125. 2010..We use this updated model to identify reactions that are subject to regulatory control in the metabolic network of G. sulfurreducens using thermodynamic variability analysis... - In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modellingRadhakrishnan Mahadevan
Department of Chemical Engineering and Applied Chemistry, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
Nat Rev Microbiol 9:39-50. 2011.... - Economics of membrane occupancy and respiro-fermentationKai Zhuang
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
Mol Syst Biol 7:500. 2011..These results suggest that the membrane occupancy constraint may be a fundamental governing constraint of cellular metabolism and physiology, and establishes a direct link between cell morphology and physiology... - Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain designKai Zhuang
Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
BMC Biotechnol 13:8. 2013..In order to address this issue, we developed the Dynamic Strain Scanning Optimization (DySScO) strategy, which integrates the Dynamic Flux Balance Analysis (dFBA) method with existing strain algorithms... - The design of long-term effective uranium bioremediation strategy using a community metabolic modelK Zhuang
Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Rm 326, Toronto, Ontario, Canada
Biotechnol Bioeng 109:2475-83. 2012..They also show that computational modeling of microbial community is an important tool to design effective strategies for practical applications in environmental biotechnology... - Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environmentsKai Zhuang
Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
ISME J 5:305-16. 2011..These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies... - EMILiO: a fast algorithm for genome-scale strain designLaurence Yang
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
Metab Eng 13:272-81. 2011..This was enabled by successive linear programming, a technique new to the area of computational strain design... - Metabolic model refinement using phenotypic microarray dataPratish Gawand
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
Methods Mol Biol 985:47-59. 2013..In this chapter, we present a protocol to refine preconstructed metabolic models using the PM data. Both manual refinement and algorithmic approaches for integrating the PM data into metabolic models have been discussed... - In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicalsAditya V Pandit
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
Microb Cell Fact 10:76. 2011..In the context of microbial fermentation, these bioelectrochemical techniques can be used to improve product yields and/or productivity... - Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessingFahimeh Salimi
Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada
Biotechnol J 5:726-38. 2010..Co-culture simulations suggest that cellobiose inhibition cannot be the main factor that is responsible for improved cellulose utilization relative to mono-culture of C. cellulolyticum... - Characterization of proton production and consumption associated with microbial metabolismKarthikeyan Srinivasan
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S3E5, Canada
BMC Biotechnol 10:2. 2010.... - Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducensDaniel Segura
Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
PLoS Comput Biol 4:e36. 2008..The results demonstrate the need to experimentally verify the activity of key enzymes when developing in silico models of microbial physiology based on sequence-based reconstruction of metabolic networks... 
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality dataYou Kwan Oh
Department of Bioengineering, University of California at San Diego, La Jolla, California 92093 0412, USA
J Biol Chem 282:28791-9. 2007..Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes...- Estimating optimal profiles of genetic alterations using constraint-based modelsKapil G Gadkar
Department of Chemical Engineering, University of California, Santa Barbara, CA 92121, USA
Biotechnol Bioeng 89:243-51. 2005..36 mmol L(-1)) and fully active acetate flux (6.22 mmol L(-1)). We also examine the effects of growth inhibition due to high ethanol concentrations and variations in final batch time on ethanol production... - Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrumSharon J Wiback
Department of Bioengineering, University of California, 9500 Gilman Drive EBU 1 Room 6607, San Diego, La Jolla, CA 92093, USA
J Theor Biol 224:313-24. 2003.... - Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrumSharon J Wiback
Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Biotechnol Bioeng 86:317-31. 2004..These predicted internal flux trends are, in general, consistent with the flux trends measured using experimental metabolic flux analysis techniques... - k-Cone analysis: determining all candidate values for kinetic parameters on a network scaleIman Famili
Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0412, USA
Biophys J 88:1616-25. 2005.... - Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch cultureJared L Hjersted
Department of Chemical Engineering, University of Massachusetts, 159 Goessmann Laboratory, 686 North Pleasant Street, Amherst, MA 01003 3110, USA
Biotechnol Bioeng 97:1190-204. 2007.... - On-line optimization of recombinant product in a fed-batch bioreactorRadhakrishnan Mahadevan
Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
Biotechnol Prog 19:639-46. 2003..The simulation results indicated improvement in the amount of product formed, when the optimal profile is regenerated during the course of the batch...