All Stories

  1. A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

    Article • Proceedings of the National Academy of Sciences, November 2022, Proceedings of the National Academy of Sciences

    Professor Vassily Hatzimanikatis

  2. The influence of the crowding assumptions in biofilm simulations

    Article • PLoS Computational Biology, July 2021, PLOS

    Professor Vassily Hatzimanikatis

  3. Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

    Article • PLoS Computational Biology, July 2021, PLOS

    Professor Vassily Hatzimanikatis

  4. Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

    Article • Proceedings of the National Academy of Sciences, February 2021, Proceedings of the National Academy of Sciences

    Professor Vassily Hatzimanikatis

  5. Statistical inference in ensemble modeling of cellular metabolism

    Article • PLoS Computational Biology, December 2019, PLOS

    Marc-Olivier Boldi, Professor Vassily Hatzimanikatis

  6. Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

    Article • PLoS Computational Biology, August 2019, PLOS

    Professor Vassily Hatzimanikatis

  7. Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

    Article • PLoS Computational Biology, May 2019, PLOS

    Professor Vassily Hatzimanikatis

  8. Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

    Article • PLoS Computational Biology, April 2019, PLOS

    Professor Vassily Hatzimanikatis

  9. Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Professor Vassily Hatzimanikatis

  10. Antihypertensive Drugs Metabolism: An Update to Pharmacokinetic Profiles and Computational Approaches

    Article • Current Pharmaceutical Design, December 2014, Bentham Science Publishers

    Professor Vassily Hatzimanikatis

  11. Kinetic models in industrial biotechnology – Improving cell factory performance

    Article • Metabolic Engineering, July 2014, Elsevier

    Professor Vassily Hatzimanikatis, Assoc Professor Mats Jirstrand

  12. A computational framework for integration of lipidomics data into metabolic pathways

    Article • Metabolic Engineering, May 2014, Elsevier

    Professor Vassily Hatzimanikatis

  13. A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism

    Article • PLoS Computational Biology, May 2014, PLOS

    Professor Vassily Hatzimanikatis

  14. Constraining the Flux Space Using Thermodynamics and Integration of Metabolomics Data

    Article • January 2014, Springer Science + Business Media

    Professor Vassily Hatzimanikatis

  15. A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor

    Article • PLoS ONE, November 2013, PLOS

    Professor Vassily Hatzimanikatis

  16. A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

    Article • PLoS Computational Biology, October 2013, PLOS

    Professor Vassily Hatzimanikatis

  17. Editorial: Metabolic modeling in biotechnology and medical research

    Article • Biotechnology Journal, September 2013, Wiley

    Professor Vassily Hatzimanikatis

  18. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

    Article • Biotechnology Journal, August 2013, Wiley

    Professor Vassily Hatzimanikatis

  19. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

    Article • Briefings in Functional Genomics, June 2013, Oxford University Press (OUP)

    Professor Vassily Hatzimanikatis

  20. Mechanistically Consistent Reduced Models of Synthetic Gene Networks

    Article • Biophysical Journal, May 2013, Elsevier

    Professor Vassily Hatzimanikatis

  21. Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

    Article • Microbial Biotechnology, January 2013, Wiley

    Professor Vassily Hatzimanikatis

  22. Exploration of trade-offs between steady-state and dynamic properties in signaling cycles

    Article • Physical Biology, August 2012, Institute of Physics Publishing

    Professor Vassily Hatzimanikatis

  23. A computational framework for the design of optimal protein synthesis

    Article • Biotechnology and Bioengineering, February 2012, Wiley

    Professor Vassily Hatzimanikatis

  24. From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

    Article • FEMS Yeast Research, December 2011, Oxford University Press (OUP)

    Professor Vassily Hatzimanikatis

  25. Integrating computational methods to retrofit enzymes to synthetic pathways

    Article • Biotechnology and Bioengineering, September 2011, Wiley

    Professor Vassily Hatzimanikatis

  26. Manipulating redox and ATP balancing for improved production of succinate in E. coli

    Article • Metabolic Engineering, January 2011, Elsevier

    Professor Vassily Hatzimanikatis

  27. Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

    Article • Biophysical Journal, November 2010, Elsevier

    Professor Vassily Hatzimanikatis

  28. Modeling of uncertainties in biochemical reactions

    Article • Biotechnology and Bioengineering, October 2010, Wiley

    Professor Vassily Hatzimanikatis

  29. DREAMS of metabolism

    Article • Trends in Biotechnology, October 2010, Elsevier

    Professor Vassily Hatzimanikatis

  30. Production of biofuels and biochemicals: in need of an ORACLE

    Article • Trends in Biotechnology, August 2010, Elsevier

    Professor Vassily Hatzimanikatis

  31. Network thermodynamics in the post-genomic era

    Article • Current Opinion in Microbiology, June 2010, Elsevier

    Professor Vassily Hatzimanikatis

  32. The Origins of Time-Delay in Template Biopolymerization Processes

    Article • PLoS Computational Biology, April 2010, PLOS

    Professor Vassily Hatzimanikatis

  33. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate

    Article • Biotechnology and Bioengineering, January 2010, Wiley

    Professor Vassily Hatzimanikatis

  34. In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

    Article • BMC Systems Biology, January 2010, Springer Science + Business Media

    Professor Vassily Hatzimanikatis

  35. Computational framework for predictive biodegradation

    Article • Biotechnology and Bioengineering, December 2009, Wiley

    Professor Vassily Hatzimanikatis

  36. Thermodynamic analysis of biodegradation pathways

    Article • Biotechnology and Bioengineering, June 2009, Wiley

    Professor Vassily Hatzimanikatis

  37. Discovery of Novel Routes for the Production of Fuels and Chemicals

    Article • June 2009, Taylor & Francis

    Professor Vassily Hatzimanikatis

  38. Effects of Codon Distributions and tRNA Competition on Protein Translation

    Article • Biophysical Journal, August 2008, Elsevier

    Professor Vassily Hatzimanikatis

  39. Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

    Article • Biophysical Journal, August 2008, Elsevier

    Professor Vassily Hatzimanikatis

  40. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

    Article • Molecular Systems Biology, June 2007, EMBO

    Professor Vassily Hatzimanikatis

  41. Thermodynamics-Based Metabolic Flux Analysis

    Article • Biophysical Journal, March 2007, Elsevier

    Professor Vassily Hatzimanikatis

  42. A Model for Protein Translation: Polysome Self-Organization Leads to Maximum Protein Synthesis Rates

    Article • Biophysical Journal, February 2007, Elsevier

    Professor Vassily Hatzimanikatis

  43. A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data

    Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Professor Vassily Hatzimanikatis

  44. Metabolic engineering under uncertainty—II: Analysis of yeast metabolism

    Article • Metabolic Engineering, March 2006, Elsevier

    Professor Vassily Hatzimanikatis

  45. Metabolic engineering under uncertainty. I: Framework development

    Article • Metabolic Engineering, March 2006, Elsevier

    Professor Vassily Hatzimanikatis

  46. An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks

    Article • Biophysical Journal, February 2006, Elsevier

    Professor Vassily Hatzimanikatis

  47. Bistability Explains Threshold Phenomena in Protein Aggregation both In Vitro and In Vivo

    Article • Biophysical Journal, February 2006, Elsevier

    Professor Vassily Hatzimanikatis

  48. Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism

    Article • Biophysical Journal, February 2006, Elsevier

    Professor Vassily Hatzimanikatis

  49. The systems engineering of cellular processes

    Article • January 2006, Elsevier

    Professor Vassily Hatzimanikatis

  50. Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors inEscherichia coli

    Article • Biotechnology and Bioengineering, January 2006, Wiley

    Professor Vassily Hatzimanikatis

  51. Extracting networks from expression data

    Article • November 2005, Wiley

    Professor Vassily Hatzimanikatis

  52. Theoretical Considerations and Computational Analysis of the Complexity in Polyketide Synthesis Pathways

    Article • Journal of the American Chemical Society, July 2005, American Chemical Society (ACS)

    Professor Vassily Hatzimanikatis

  53. Mathematical Modeling of the Eukaryotic Heat-Shock Response: Dynamics of the hsp70 Promoter

    Article • Biophysical Journal, March 2005, Elsevier

    Professor Vassily Hatzimanikatis

  54. Exploring the diversity of complex metabolic networks

    Article • Bioinformatics, December 2004, Oxford University Press (OUP)

    Professor Vassily Hatzimanikatis

  55. Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies

    Article • Biophysical Journal, December 2004, Elsevier

    Professor Vassily Hatzimanikatis

  56. Computational discovery of biochemical routes to specialty chemicals

    Article • Chemical Engineering Science, November 2004, Elsevier

    Professor Vassily Hatzimanikatis

  57. A model-based optimization framework for the inference on gene regulatory networks from DNA array data

    Article • Bioinformatics, July 2004, Oxford University Press (OUP)

    Professor Vassily Hatzimanikatis

  58. Metabolic networks: enzyme function and metabolite structure

    Article • Current Opinion in Structural Biology, June 2004, Elsevier

    Professor Vassily Hatzimanikatis

  59. Insights into the relation between mRNA and protein expression patterns: I. theoretical considerations

    Article • Biotechnology and Bioengineering, December 2003, Wiley

    Professor Vassily Hatzimanikatis

  60. Insights into the relation between mrna and protein expression patterns: ii. Experimental observations inEscherichia coli

    Article • Biotechnology and Bioengineering, December 2003, Wiley

    Professor Vassily Hatzimanikatis

  61. Integration of Proteomic, Genechip, and DNA Sequence Data

    Article • August 2003, Taylor & Francis

    Professor Vassily Hatzimanikatis

  62. Jay Bailey as mentor?The students' perspective

    Article • Biotechnology and Bioengineering, July 2002, Wiley

    Professor Vassily Hatzimanikatis

  63. A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering

    Article • Biotechnology and Bioengineering, July 2002, Wiley

    Professor Vassily Hatzimanikatis

  64. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes

    Article • Biotechnology and Bioengineering, July 2002, Wiley

    Professor Vassily Hatzimanikatis

  65. A mathematical description of regulation of the G1‐S transition of the mammalian cell cycle

    Article • Biotechnology and Bioengineering, December 1999, Wiley

    Professor Vassily Hatzimanikatis

  66. A mathematical description of regulation of the G1-S transition of the mammalian cell cycle

    Article • Biotechnology and Bioengineering, December 1999, Wiley

    Professor Vassily Hatzimanikatis

  67. Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information

    Article • Metabolic Engineering, October 1999, Elsevier

    Professor Vassily Hatzimanikatis

  68. Proteomics: Theoretical and Experimental Considerations

    Article • Biotechnology Progress, June 1999, Wiley

    Professor Vassily Hatzimanikatis

  69. Modelling molecular mechanisms within their cellular environment

    Article • Journal of Biotechnology, May 1999, Elsevier

    Professor Vassily Hatzimanikatis

  70. Nonlinear Metabolic Control Analysis

    Article • Metabolic Engineering, January 1999, Elsevier

    Professor Vassily Hatzimanikatis

  71. Application of mathematical tools for metabolic design of microbial ethanol production

    Article • Biotechnology and Bioengineering, April 1998, Wiley

    Professor Vassily Hatzimanikatis

  72. Metabolic Consequences of Phosphotransferase (PTS) Mutation in a Phenylalanine-Producing Recombinant Escherichia coli

    Article • Biotechnology Progress, December 1997, Wiley

    Professor Vassily Hatzimanikatis

  73. Studies on glycolysis — I. Multiple steady states in bacterial glycolysis

    Article • Chemical Engineering Science, August 1997, Elsevier

    Professor Vassily Hatzimanikatis

  74. Metabolic fluxes in riboflavin-producing Bacillus subtilis

    Article • Nature Biotechnology, May 1997, Springer Science + Business Media

    Professor Vassily Hatzimanikatis

  75. Effects of spatiotemporal variations on metabolic control: Approximate analysis using (log)linear kinetic models

    Article • Biotechnology and Bioengineering, April 1997, Wiley

    Professor Vassily Hatzimanikatis

  76. The AlkB Monooxygenase of Pseudomonas oleovorans. Synthesis, Stability and Level in Recombinant Escherichia coli and the Native Host

    Article • European Journal of Biochemistry, March 1997, Wiley

    Professor Vassily Hatzimanikatis

  77. Optimization of regulatory architectures in metabolic reaction networks

    Article • Biotechnology and Bioengineering, November 1996, Wiley

    Professor Vassily Hatzimanikatis

  78. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes

    Article • Biotechnology and Bioengineering, October 1996, Wiley

    Professor Vassily Hatzimanikatis

  79. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes

    Article • Biotechnology and Bioengineering, October 1996, Wiley

    Professor Vassily Hatzimanikatis

  80. MCA Has More to Say

    Article • Journal of Theoretical Biology, October 1996, Elsevier

    Professor Vassily Hatzimanikatis

  81. Metabolic flux analysis of hybridoma cells in different culture media using mass balances

    Article • Biotechnology and Bioengineering, May 1996, Wiley

    Professor Vassily Hatzimanikatis

  82. Analysis and design of metabolic reaction networks via mixed-integer linear optimization

    Article • AIChE Journal, May 1996, Wiley

    Professor Vassily Hatzimanikatis

  83. Effect ofVitreoscilla hemoglobin dosage on microaerobicEscherichia coli carbon and energy metabolism

    Article • Biotechnology and Bioengineering, January 1996, Wiley

    Professor Vassily Hatzimanikatis

  84. Effect of Vitreoscilla hemoglobin dosage on microaerobic Escherichia coli carbon and energy metabolism

    Article • Biotechnology and Bioengineering, January 1996, Wiley

    Professor Vassily Hatzimanikatis

  85. Recombinant cyclin E expression activates proliferation and obviates surface attachment of chinese hamster ovary (CHO) cells in protein-free medium

    Article • Biotechnology and Bioengineering, August 1995, Wiley

    Professor Vassily Hatzimanikatis

  86. A mathematical model for the G1/S transition of the mammalian cell cycle

    Article • Biotechnology Letters, July 1995, Springer Science + Business Media

    Professor Vassily Hatzimanikatis

  87. A method for pulsed periodic optimization of chemical reaction systems

    Article • Chemical Engineering Science, February 1993, Elsevier

    Professor Vassily Hatzimanikatis

  88. Communicating in software engineering environments: The GRASPIN paradigm

    Article • Journal of Systems and Software, April 1991, Elsevier

    Professor Vassily Hatzimanikatis

  89. Modeling and control of intracellular processes

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Vassily Hatzimanikatis

  90. DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Vassily Hatzimanikatis