Radhakrishnan Mahadevan

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. doi request reprint Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis
    Radhakrishnan Mahadevan
    Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
    OMICS 12:33-59. 2008
  2. doi request reprint Characterizing metabolic interactions in a clostridial co-culture for consolidated bioprocessing
    Fahimeh Salimi
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 2E6, Canada
    BMC Biotechnol 13:95. 2013
  3. pmc Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
    Hitoshi Suzuki
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
    BMC Genomics 13:444. 2012
  4. pmc Genome-scale constraint-based modeling of Geobacter metallireducens
    Jun Sun
    Genomatica Inc, San Diego, CA, USA
    BMC Syst Biol 3:15. 2009
  5. pmc Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
    Carla Risso
    Department of Microbiology, 203N Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA
    BMC Genomics 10:447. 2009
  6. pmc The degree of redundancy in metabolic genes is linked to mode of metabolism
    R 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
  7. doi request reprint In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
    Radhakrishnan 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
  8. pmc Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling
    Srinath Garg
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario M5S3E5, Canada
    BMC Res Notes 3:125. 2010
  9. pmc Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design
    Kai Zhuang
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
    BMC Biotechnol 13:8. 2013
  10. doi request reprint Metabolic model refinement using phenotypic microarray data
    Pratish Gawand
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 985:47-59. 2013

Collaborators

  • Michael A Henson
  • Alison P McGuigan
  • Alexei Savchenko
  • Hideki Kobayashi
  • Julia Krushkal
  • Mounir Izallalen
  • Hanno Richter
  • Carla Risso
  • Barbara A Methe
  • Bernhard Ø Palsson
  • D R Lovley
  • E Ma
  • M V Coppi
  • Jeremy S Edwards
  • K P Nevin
  • Christophe H Schilling
  • Kai Zhuang
  • Laurence Yang
  • William R Cluett
  • Nikolaos Anesiadis
  • Pratish Gawand
  • Fahimeh Salimi
  • Sharon J Wiback
  • Iman Famili
  • Sahar Javaherian
  • Hongyan Zheng
  • Hitoshi Suzuki
  • K Zhuang
  • Aditya V Pandit
  • Karthikeyan Srinivasan
  • Srinath Garg
  • Jun Sun
  • Daniel Segura
  • You Kwan Oh
  • Jared L Hjersted
  • Kapil G Gadkar
  • Zdzislaw Wawrzak
  • Andrew Ekins
  • Wayne F Anderson
  • Vincent J J Martin
  • Robert Flick
  • Greg Brown
  • Anatoli Tchigvintsev
  • Patrick Hyland
  • Alina Beliavsky
  • Alexander F Yakunin
  • Joseph S Brunzelle
  • Elena Evdokimova
  • Erika Lindquist
  • Pedro Coutinho
  • Khajamohiddin Syed
  • Patricia A vanKuyk
  • Emma R Master
  • Asaf Salamov
  • Kurt LaButti
  • Kerrie Barry
  • Ronald P de Vries
  • Alla Lapidus
  • Kiyohiko Igarashi
  • Masahiro Samejima
  • Susan Lucas
  • Yunchen Gong
  • Jagjit S Yadav
  • Bernard Henrissat
  • Igor V Grigoriev
  • Mamdouh Abou-Zaid
  • Andrea Aerts
  • Ad Wiebenga
  • Jacqueline MacDonald
  • Chiaki Hori
  • Paula Mouser
  • Goutham N Vemuri
  • TOM R FAHLAND
  • Jessica E Butler
  • Priti Pharkya
  • Bahareh Sayyar
  • Katy Juarez
  • Sung M Park
  • Francis J Doyle Iii

Detail Information

Publications30

  1. doi request reprint Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis
    Radhakrishnan 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...
  2. doi request reprint Characterizing metabolic interactions in a clostridial co-culture for consolidated bioprocessing
    Fahimeh Salimi
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 2E6, Canada
    BMC Biotechnol 13:95. 2013
    ..However, the metabolic interactions in this co-culture are not well understood. To investigate the metabolic interactions in this co-culture we dynamically characterized the physiology and microbial composition using qPCR...
  3. pmc Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
    Hitoshi Suzuki
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
    BMC Genomics 13:444. 2012
    ..To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome...
  4. pmc Genome-scale constraint-based modeling of Geobacter metallireducens
    Jun 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...
  5. pmc Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
    Carla 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...
  6. pmc The degree of redundancy in metabolic genes is linked to mode of metabolism
    R 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...
  7. doi request reprint In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
    Radhakrishnan 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
    ....
  8. pmc Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling
    Srinath 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...
  9. pmc Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design
    Kai 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...
  10. doi request reprint Metabolic model refinement using phenotypic microarray data
    Pratish 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...
  11. pmc Economics of membrane occupancy and respiro-fermentation
    Kai 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...
  12. doi request reprint The design of long-term effective uranium bioremediation strategy using a community metabolic model
    K 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...
  13. pmc Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
    Kai 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...
  14. doi request reprint Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
    Fahimeh 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...
  15. doi request reprint EMILiO: a fast algorithm for genome-scale strain design
    Laurence 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...
  16. doi request reprint Analysis and design of a genetic circuit for dynamic metabolic engineering
    Nikolaos Anesiadis
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada, M5S 3E5
    ACS Synth Biol 2:442-52. 2013
    ..This analysis can now be used to guide the experimental implementation of a dynamic metabolic engineering strategy and reduce the time required to design the genetic circuit components. ..
  17. pmc In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicals
    Aditya 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...
  18. pmc Characterization of proton production and consumption associated with microbial metabolism
    Karthikeyan Srinivasan
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S3E5, Canada
    BMC Biotechnol 10:2. 2010
    ....
  19. doi request reprint Novel approach to engineer strains for simultaneous sugar utilization
    Pratish Gawand
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, Canada M5S 3E5
    Metab Eng 20:63-72. 2013
    ..Furthermore, sequencing studies on the genes involved in CCR showed that the mechanism for co-utilization of the sugars could be different from previously known mechanisms. ..
  20. doi request reprint Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium
    Hongyan Zheng
    Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Proteins 81:1031-41. 2013
    ..Our work has provided further insight into the molecular mechanisms of substrate selectivity and activity of succinate semialdehyde dehydrogenases...
  21. doi request reprint Dynamic metabolic engineering for increasing bioprocess productivity
    Nikolaos Anesiadis
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ont, Canada M5S3E5
    Metab Eng 10:255-66. 2008
    ..We have designed and analyzed an integrated computational model for the dynamic control of gene expression. This controller, when coupled to the metabolism of E. coli, resulted in increased bioprocess productivity...
  22. doi request reprint Design principles for generating robust gene expression patterns in dynamic engineered tissues
    Sahar Javaherian
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, ON M5S 3E5, Canada
    Integr Biol (Camb) 5:578-89. 2013
    ..Our results highlight the importance of coordinating gene induction dynamics and cellular movement in order to achieve robust pattern formation...
  23. ncbi request reprint Estimating optimal profiles of genetic alterations using constraint-based models
    Kapil 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...
  24. ncbi request reprint Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
    You 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...
  25. pmc Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens
    Daniel 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...
  26. pmc k-Cone analysis: determining all candidate values for kinetic parameters on a network scale
    Iman Famili
    Department of Bioengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0412, USA
    Biophys J 88:1616-25. 2005
    ....
  27. ncbi request reprint Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture
    Jared 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
    ....
  28. ncbi request reprint Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum
    Sharon 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...
  29. ncbi request reprint Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum
    Sharon 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
    ....
  30. ncbi request reprint On-line optimization of recombinant product in a fed-batch bioreactor
    Radhakrishnan 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...