Vassily Hatzimanikatis

Summary

Affiliation: Northwestern University
Country: USA

Publications

  1. ncbi request reprint Exploring the diversity of complex metabolic networks
    Vassily Hatzimanikatis
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
    Bioinformatics 21:1603-9. 2005
  2. ncbi request reprint Metabolic engineering under uncertainty. I: framework development
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Room E136, Evanston, IL 60208 3120, USA
    Metab Eng 8:133-41. 2006
  3. ncbi request reprint A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering
    Vassily Hatzimanikatis
    Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208 3120, USA
    Biotechnol Bioeng 79:504-8. 2002
  4. ncbi request reprint Metabolic networks: enzyme function and metabolite structure
    Vassily Hatzimanikatis
    Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, E136, Evanston, Illinois 60208 3120, USA
    Curr Opin Struct Biol 14:300-6. 2004
  5. pmc An algorithmic framework for genome-wide modeling and analysis of translation networks
    Amit Mehra
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:1136-46. 2006
  6. pmc The origins of time-delay in template biopolymerization processes
    Luis Mier-y-Teran-Romero
    Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
    PLoS Comput Biol 6:e1000726. 2010
  7. pmc Genome-scale thermodynamic analysis of Escherichia coli metabolism
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:1453-61. 2006
  8. pmc Thermodynamics-based metabolic flux analysis
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 92:1792-805. 2007
  9. pmc Effects of codon distributions and tRNA competition on protein translation
    Hermioni Zouridis
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 95:1018-33. 2008
  10. pmc Metabolic control analysis under uncertainty: framework development and case studies
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60616, USA
    Biophys J 87:3750-63. 2004

Research Grants

  1. Topical Conference: Systems Biol & Metabolic Engineering
    Vassily Hatzimanikatis; Fiscal Year: 2003

Collaborators

Detail Information

Publications27

  1. ncbi request reprint Exploring the diversity of complex metabolic networks
    Vassily Hatzimanikatis
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
    Bioinformatics 21:1603-9. 2005
    ....
  2. ncbi request reprint Metabolic engineering under uncertainty. I: framework development
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Room E136, Evanston, IL 60208 3120, USA
    Metab Eng 8:133-41. 2006
    ..Hatzimanikatis, V., 2005. Metabolic engineering under uncertainty. II: analysis of yeast metabolism. Submitted]...
  3. ncbi request reprint A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering
    Vassily Hatzimanikatis
    Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208 3120, USA
    Biotechnol Bioeng 79:504-8. 2002
    ..This short review is by no means complete and provides only a partial view of Jay's contribution to the metabolic engineering of prokaryotes...
  4. ncbi request reprint Metabolic networks: enzyme function and metabolite structure
    Vassily Hatzimanikatis
    Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, E136, Evanston, Illinois 60208 3120, USA
    Curr Opin Struct Biol 14:300-6. 2004
    ....
  5. pmc An algorithmic framework for genome-wide modeling and analysis of translation networks
    Amit Mehra
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:1136-46. 2006
    ..Such quantitative understanding of the sensitivity of protein synthesis to the variation of mRNA expression can provide insights into cellular robustness mechanisms and guide the design of protein production systems...
  6. pmc The origins of time-delay in template biopolymerization processes
    Luis Mier-y-Teran-Romero
    Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
    PLoS Comput Biol 6:e1000726. 2010
    ....
  7. pmc Genome-scale thermodynamic analysis of Escherichia coli metabolism
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:1453-61. 2006
    ..The methodologies and results discussed can be used to facilitate the refinement of the feasible ranges for cellular parameters such as species concentrations and reaction rate constants...
  8. pmc Thermodynamics-based metabolic flux analysis
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 92:1792-805. 2007
    ..Further, we find that the NAD/NADH and NADP/NADPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively...
  9. pmc Effects of codon distributions and tRNA competition on protein translation
    Hermioni Zouridis
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 95:1018-33. 2008
    ..Along these lines, we find that the relative position of codons along the mRNA determines the optimal protein synthesis rate...
  10. pmc Metabolic control analysis under uncertainty: framework development and case studies
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60616, USA
    Biophys J 87:3750-63. 2004
    ....
  11. pmc Computational framework for predictive biodegradation
    Stacey D Finley
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
    Biotechnol Bioeng 104:1086-97. 2009
    ..This work demonstrates that BNICE can be applied to generate novel pathways to degrade xenobiotic compounds that are thermodynamically feasible alternatives to known biodegradation routes and attractive targets for metabolic engineering...
  12. ncbi request reprint Metabolic engineering under uncertainty--II: analysis of yeast metabolism
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Room E136, Evanston, IL 60208 3120, USA
    Metab Eng 8:142-59. 2006
    ..Clustering of the reaction steps according to the similarity of their responses to enzyme activity perturbations reveals functional coupling of metabolic reactions...
  13. pmc In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene
    Stacey D Finley
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, USA
    BMC Syst Biol 4:7. 2010
    ..However, given the wealth of novel pathways obtained using these prediction methods, it is necessary to evaluate their relative feasibility, particularly within the context of the cellular environment...
  14. doi request reprint Manipulating redox and ATP balancing for improved production of succinate in E. coli
    Amarjeet Singh
    Department of Chemical and Biological Engineering, University of Colorado, UCB 424, Boulder, CO 80309, USA
    Metab Eng 13:76-81. 2011
    ..Testing of this prediction confirmed that PEPCK overexpression resulted in a 60% increase in biomass and succinate formation in the ldhA, pflB, ptsG mutant strain...
  15. pmc Bistability explains threshold phenomena in protein aggregation both in vitro and in vivo
    Theodore R Rieger
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:886-95. 2006
    ..Therefore, our results offer a possible theoretical explanation for neuronal vulnerability observed in vivo and the onset of neurodegenerative phenotypes in neurons lacking an effective heat-shock response...
  16. doi request reprint Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    Christopher S Henry
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
    Biotechnol Bioeng 106:462-73. 2010
    ..Examination of the optimal pathways for the biosynthesis of these 28 compounds in E. coli revealed pyruvate and succinate to be ideal intermediates for achieving high product yields from glucose...
  17. ncbi request reprint Jay Bailey as mentor--the students' perspective
    Kenneth F Reardon
    Department of Chemical Engineering, Colorado State University, Fort Collins 80523 1370, USA
    Biotechnol Bioeng 79:484-9. 2002
    ..Jay's contributions as a mentor can perhaps be recognized as being as significant as his research achievements...
  18. ncbi request reprint Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli
    Joanna González-Lergier
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
    Biotechnol Bioeng 95:638-44. 2006
    ....
  19. pmc A model for protein translation: polysome self-organization leads to maximum protein synthesis rates
    Hermioni Zouridis
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 92:717-30. 2007
    ....
  20. pmc Thermodynamic analysis of biodegradation pathways
    Stacey D Finley
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois 60208, USA
    Biotechnol Bioeng 103:532-41. 2009
    ..This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways...
  21. ncbi request reprint Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations
    Amit Mehra
    Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208, USA
    Biotechnol Bioeng 84:822-33. 2003
    ....
  22. ncbi request reprint Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways
    Joanna González-Lergier
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
    J Am Chem Soc 127:9930-8. 2005
    ..Consequently, this formulation would prove useful in guiding experimental approaches to engineer novel polyketides, a number of which will likely have medicinal properties...
  23. ncbi request reprint A model-based optimization framework for the inference on gene regulatory networks from DNA array data
    Reuben Thomas
    Department of Industrial Engineering and Management Science, Northwestern University, Evanston, IL 60208 3120, USA
    Bioinformatics 20:3221-35. 2004
    ....
  24. pmc Mathematical modeling of the eukaryotic heat-shock response: dynamics of the hsp70 promoter
    Theodore R Rieger
    Department of Chemical and Biological Engineering, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, USA
    Biophys J 88:1646-58. 2005
    ....
  25. pmc A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Adam M Feist
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Syst Biol 3:121. 2007
    ..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
  26. ncbi request reprint Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes
    James E Bailey
    Institute of Biotechnology, ETH Zurich, Switzerland
    Biotechnol Bioeng 79:568-79. 2002
    ..This paradigm has been successfully applied in several contexts, including elimination of growth factor requirements in mammalian cell culture and increasing the energetic efficiency of microaerobic bacterial respiration...
  27. pmc Group contribution method for thermodynamic analysis of complex metabolic networks
    Matthew D Jankowski
    Mayo Clinic, Rochester, Minnesota 55905, USA
    Biophys J 95:1487-99. 2008
    ..A web-based implementation of this new group contribution method is available free at http://sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi...

Research Grants1

  1. Topical Conference: Systems Biol & Metabolic Engineering
    Vassily Hatzimanikatis; Fiscal Year: 2003
    ..The conference will also provide 4 fellowships to graduate students for attending the conference. ..