Journal Papers

2019

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

V. Pandey; N. Hadadi; V. Hatzimanikatis 

PLOS Computational Biology. 2019-05-13. Vol. 15, num. 5, p. e1007036. DOI : 10.1371/journal.pcbi.1007036.

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

L. Miskovic; M. Tokic; G. Savoglidis; V. Hatzimanikatis 

Industrial & Engineering Chemistry Research. 2019-05-10. DOI : 10.1021/acs.iecr.9b00818.

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

V. Pandey; V. Hatzimanikatis 

PLOS Computational Biology. 2019-04-19. Vol. 15, num. 4, p. e1006760. DOI : 10.1371/journal.pcbi.1006760.

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

C. List; Z. Hosseini; K. Lederballe Meibom; V. Hatzimanikatis; R. Bernier‐Latmani 

Environmental Microbiology. 2019. DOI : 10.1111/1462-2920.14640.

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

N. Hadadi; H. MohammadiPeyhani; L. Miskovic; M. Seijo; V. Hatzimanikatis 

Proceedings of the National Academy of Sciences. 2019.  p. 201818877. DOI : 10.1073/pnas.1818877116.

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

T. E. Hameri; G. Fengos; M. Ataman; L. Miskovic; V. Hatzimanikatis 

Metabolic Engineering. 2019. Vol. 52, p. 29-41. DOI : 10.1016/j.ymben.2018.10.005.

2018

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

M. Tokic; N. Hadadi; M. Ataman; D. Neves; B. E. Ebert et al. 

ACS Synthetic Biology. 2018-07-18. Vol. 7, num. 8, p. 1858-1873. DOI : 10.1021/acssynbio.8b00049.

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

P. Salvy; G. Fengos; M. Ataman; T. Pathier; K. C. Soh et al. 

Bioinformatics. 2018-07-02.  p. 1-3. DOI : 10.1093/bioinformatics/bty499.

2017

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

L. C. Bryan; D. R. Weilandt; A. L. Bachmann; S. Kilic; C. C. Lechner et al. 

Nucleic Acids Research. 2017.  p. gkx697. DOI : 10.1093/nar/gkx697.

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

M. Ataman; D. F. H. Gardiol; G. Fengos; V. Hatzimanikatis 

Plos Computational Biology. 2017. Vol. 13, num. 7, p. e1005444. DOI : 10.1371/journal.pcbi.1005444.

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

M. Ataman; V. Hatzimanikatis 

Plos Computational Biology. 2017. Vol. 13, num. 7, p. e1005513. DOI : 10.1371/journal.pcbi.1005513.

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

M. A. Islam; N. Hadadi; M. Ataman; V. Hatzimanikatis; G. Stephanopoulos 

Metabolic Engineering. 2017. Vol. 41, p. 173-181. DOI : 10.1016/j.ymben.2017.04.005.

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

Y. Berset; D. Merulla; A. Joublin; V. Hatzimanikatis; J. R. Van Der Meer 

Acs Synthetic Biology. 2017. Vol. 6, num. 5, p. 862-874. DOI : 10.1021/acs.synbio.6b00364.

On Lewis acidity/basicity and hydrogen bonding in the equation-of-state approach

C. Panayiotou; S. Mastrogeorgopoulos; V. Hatzimanikatis 

Journal Of Chemical Thermodynamics. 2017. Vol. 110, p. 3-15. DOI : 10.1016/j.jct.2017.02.003.

Redefining solubility parameters: Bulk and surface properties from unified molecular descriptors

C. Panayiotou; S. Mastrogeorgopoulos; D. Aslanidou; M. Avgidou; V. Hatzimanikatis 

Journal Of Chemical Thermodynamics. 2017. Vol. 111, p. 207-220. DOI : 10.1016/j.jct.2017.03.035.

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

L. Miskovic; S. Alff-Tuomala; K. C. Soh; D. Barth; L. Salusjärvi et al. 

Biotechology for Biofuels. 2017. Vol. 10, p. 166. DOI : 10.1186/s13068-017-0838-5.

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

A. Kiparissides; V. Hatzimanikatis 

Metabolic Engineering. 2017. Vol. 39, p. 117-127. DOI : 10.1016/j.ymben.2016.11.006.

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

A. Chiappino Pepe; S. Tymoshenko; M. Ataman; D. Soldati-Favre; V. Hatzimanikatis 

PLoS Computational Biology. 2017. Vol. 13, num. 3. DOI : 10.1371/journal.pcbi.1005397.

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

N. Hadadi; J. Hafner; K. C. Soh; V. Hatzimanikatis 

Biotechnology Journal. 2017. Vol. 12, num. 1, p. 1600464. DOI : 10.1002/biot.201600464.

2016

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

C. Panayiotou; S. Mastrogeorgopoulos; M. Ataman; N. Hadadi; V. Hatzimanikatis 

Physical Chemistry Chemical Physics -Cambridge- Royal Society of Chemistry. 2016. Vol. 18, num. 47, p. 32570-32592. DOI : 10.1039/C6CP06281D.

Principles of Systems Biology, No. 11

G. Wayne; A. Graves; D. Hassabis; S. Saha; C. A. Weber et al. 

Cell Systems. 2016. Vol. 3, num. 5, p. 406-410.

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

C. Panayiotou; S. Mastrogeorgopoulos; M. Ataman; N. Hadadi; V. Hatzimanikatis 

Physical Chemistry Chemical Physics. 2016. Vol. 18, num. 47, p. 32570-32592. DOI : 10.1039/c6cp06281d.

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

N. Hadadi; J. Hafner; A. Shajkofci; A. Zisaki; V. Hatzimanikatis 

Acs Synthetic Biology. 2016. Vol. 5, num. 10, p. 1155-1166. DOI : 10.1021/acssynbio.6b00054.

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

J. Pinto Vieira; J. Racle; V. Hatzimanikatis 

Biophysical Journal. 2016. Vol. 110, num. 9, p. 2120-2131. DOI : 10.1016/j.bpj.2016.04.004.

Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering

M. Morales; M. Ataman; S. Badr; S. Linster; I. Kourlimpinis et al. 

Energy & Environmental Science. 2016. Vol. 9, num. 9, p. 2794-2805. DOI : 10.1039/c6ee00634e.

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

A. Isakova; Y. Berset; V. Hatzimanikatis; B. Deplancke 

Journal Of Biological Chemistry. 2016. Vol. 291, num. 19, p. 10293-+. DOI : 10.1074/jbc.M115.691154.

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

G. Savoglidis; A. X. D. S. Dos Santos; I. Riezman; P. Angelino; H. Riezman et al. 

Metabolic Engineering. 2016. Vol. 37, p. 46-62. DOI : 10.1016/j.ymben.2016.04.002.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

L. A. Bultet; J. Aguilar Rodriguez; C. H. Ahrens; E. L. Ahrne; N. Ai et al. 

Nucleic Acids Research. 2016. Vol. 44, num. D1, p. D27-D37. DOI : 10.1093/nar/gkv1310.

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

T. Dallavilla; L. Abrami; P. A. Sandoz; G. Savoglidis; V. Hatzimanikatis et al. 

PLOS Computational Biology. 2016. Vol. 12, num. 2, p. e1004774. DOI : 10.1371/journal.pcbi.1004774.

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

S. Andreozzi; A. Charkrabarti; K. C. Soh; A. Burgard; T-H. Yang et al. 

Metabolic Engineering. 2016. Vol. 35, p. 148-159. DOI : 10.1016/j.ymben.2016.01.009.

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

S. Andreozzi; L. Miskovic; V. Hatzimanikatis 

Metabolic Engineering. 2016. Vol. 33, p. 158-168. DOI : 10.1016/j.ymben.2015.10.002.

2015

Do genome-scale models need exact solvers or clearer standards?

A. Ebrahim; E. Almaas; E. Bauer; A. Bordbar; A. P. Burgard et al. 

Molecular Systems Biology. 2015. Vol. 11, num. 10, p. 831. DOI : 10.15252/msb.20156157.

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

M. Ataman; V. Hatzimanikatis 

Current Opinion in Biotechnology. 2015. Vol. 36, p. 176-182. DOI : 10.1016/j.copbio.2015.08.021.

Integrative approaches for signalling and metabolic networks

V. Hatzimanikatis; J. Saez-Rodriguez 

Integrative Biology. 2015. Vol. 7, num. 8, p. 844-845. DOI : 10.1039/c5ib90030a.

Solvation quantities from a COSMO-RS equation of state

C. Panayiotou; I. Tsivintzelis; D. Aslanidou; V. Hatzimanikatis 

Journal Of Chemical Thermodynamics. 2015. Vol. 90, p. 294-309. DOI : 10.1016/j.jct.2015.07.011.

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

L. Miskovic; M. Tokic; G. Fengos; V. Hatzimanikatis 

Current Opinion in Biotechnology. 2015. Vol. 36, p. 146-153. DOI : 10.1016/j.copbio.2015.08.019.

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

J. Racle; A. J. Stefaniuk; V. Hatzimanikatis 

The Journal of Chemical Physics. 2015. Vol. 143, num. 4, p. 044109. DOI : 10.1063/1.4926536.

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

N. Hadadi; M. Ataman; V. Hatzimanikatis; C. Panayiotou 

Physical Chemistry Chemical Physics. 2015. Vol. 17, num. 16, p. 10438-10453. DOI : 10.1039/c4cp05825a.

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

S. Tymoshenko; R. D. Oppenheim; R. Agren; J. Nielsen; D. Soldati-Favre et al. 

PLOS Computational Biology. 2015. Vol. 11, num. 5, p. e1004261. DOI : 10.1371/journal.pcbi.1004261.

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

A. Zisaki; L. Miskovic; V. Hatzimanikatis 

Current Pharmaceutical Design. 2015. Vol. 21, num. 6, p. 806-822.

2014

Kinetic models in industrial biotechnology - Improving cell factory performance

J. Almquist; M. Cvijovic; V. Hatzimanikatis; J. Nielsen; M. Jirstrand 

Metabolic Engineering. 2014. Vol. 24, p. 38-60. DOI : 10.1016/j.ymben.2014.03.007.

A computational framework for integration of lipidomics data into metabolic pathways

N. Hadadi; K. Cher Soh; M. Seijo; A. Zisaki; X. Guan et al. 

Metabolic engineering. 2014. Vol. 23, p. 1-8. DOI : 10.1016/j.ymben.2013.12.007.

2013

Metabolic modeling in biotechnology and medical research

D. Mattanovich; V. Hatzimanikatis 

Biotechnology Journal. 2013. Vol. 8, num. 9, p. 962-963. DOI : 10.1002/biot.201300378.

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

I. Fierro-Monti; J. Racle; C. Hernandez; P. Waridel; V. Hatzimanikatis et al. 

Plos One. 2013. Vol. 8, num. 11, p. e80423. DOI : 10.1371/journal.pone.0080423.

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

J. Racle; F. Picard; L. Girbal; M. Cocaign-Bousquet; V. Hatzimanikatis 

Plos Computational Biology. 2013. Vol. 9, num. 10, p. e1003240. DOI : 10.1371/journal.pcbi.1003240.

Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy

I. Fierro-Monti; P. Echeverria; J. Racle; C. Hernandez; D. Picard et al. 

Plos One. 2013. Vol. 8, num. 11, p. e80425. DOI : 10.1371/journal.pone.0080425.

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

D. Merulla; V. Hatzimanikatis; J. R. Van Der Meer 

Microbial Biotechnology. 2013. Vol. 6, num. 5, p. 503-514. DOI : 10.1111/1751-7915.12031.

Mechanistically Consistent Reduced Models of Synthetic Gene Networks

L. Mier-Y-Teran-Romero; M. Silber; V. Hatzimanikatis 

Biophysical Journal. 2013. Vol. 104, num. 9, p. 2098-2109. DOI : 10.1016/j.bpj.2013.03.031.

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

S. Tymoshenko; R. Oppenheim; D. Soldati-Favre; V. Hatzimanikatis 

Briefings in Functional Genomics. 2013. Vol. 12, num. 4, p. 316-327. DOI : 10.1093/bfgp/elt017.

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

A. Chakrabarti; L. Miskovic; K. C. Soh; V. Hatzimanikatis 

Biotechnology Journal. 2013. Vol. 8, num. 9, p. 1043-1057. DOI : 10.1002/biot.201300091.

2012

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

A. Radivojevic; B. Chachuat; D. Bonvin; V. Hatzimanikatis 

Physical Biology. 2012. Vol. 9, num. 4, p. 045010. DOI : 10.1088/1478-3975/9/4/045010.

A computational framework for the design of optimal protein synthesis

J. Racle; J. Overney; V. Hatzimanikatis 

Biotechnology and Bioengineering. 2012. Vol. 109, num. 8, p. 2127-2133. DOI : 10.1002/bit.24463.

Integrating computational methods to retrofit enzymes to synthetic pathways

E. Brunk; M. Neri; I. Tavernelli; V. Hatzimanikatis; U. Rothlisberger 

Biotechnology and Bioengineering. 2012. Vol. 109, p. 572-582. DOI : 10.1002/bit.23334.

2011

Systems biology

R. Kishony; V. Hatzimanikatis 

Current Opinion In Biotechnology. 2011. Vol. 22, p. 538-540. DOI : 10.1016/j.copbio.2011.06.001.

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

K. C. Soh; L. Miskovic; V. Hatzimanikatis 

FEMS Yeast Research. 2011. Vol. 12, num. 2, p. 129-143. DOI : 10.1111/j.1567-1364.2011.00771.x.

Predictions on heat transport and plasma rotation from global gyrokinetic simulations

Y. Sarazin; V. Grandgirard; J. Abiteboul; S. Allfrey; X. Garbet et al. 

Nuclear Fusion. 2011. Vol. 51, num. 10, p. 103023. DOI : 10.1088/0029-5515/51/10/103023.

2010

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

S. D. Finley; L. J. Broadbelt; V. Hatzimanikatis 

Bmc Systems Biology. 2010. Vol. 4, p. -. DOI : 10.1186/1752-0509-4-7.

Discovery and Analysis of Novel Metabolic Pathways for the Biosynthesis of Industrial Chemicals: 3-Hydroxypropanoate

C. S. Henry; L. J. Broadbelt; V. Hatzimanikatis 

Biotechnology And Bioengineering. 2010. Vol. 106, p. 462-473. DOI : 10.1002/bit.22673.

The Origins of Time-Delay in Template Biopolymerization Processes

L. Mier-y-Teran-Romero; M. Silber; V. Hatzimanikatis 

Plos Computational Biology. 2010. Vol. 6, num. 4, p. e1000726. DOI : 10.1371/journal.pcbi.1000726.

Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

S. J. Jol; A. Kuemmel; V. Hatzimanikatis; D. A. Beard; M. Heinemann 

Biophysical Journal. 2010. Vol. 99, p. 3139-3144. DOI : 10.1016/j.bpj.2010.09.043.

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

A. Singh; K. C. Soh; V. Hatzimanikatis; R. T. Gill 

Metabolic Engineering. 2010. Vol. 13, num. 1, p. 76-81. DOI : 10.1016/j.ymben.2010.10.006.

Modeling of uncertainties in biochemical reactions

L. Miskovic; V. Hatzimanikatis 

Biotechnology and Bioengineering. 2010. Vol. 108, num. 2, p. 413-423. DOI : 10.1002/bit.22932.

DREAMS of metabolism

K. C. Soh; V. Hatzimanikatis 

Trends in Biotechnology. 2010. Vol. 28, num. 10, p. 501-508. DOI : 10.1016/j.tibtech.2010.07.002.

Network thermodynamics in the post-genomic era

K. C. Soh; V. Hatzimanikatis 

Current opinion in microbiology. 2010. Vol. 13, num. 3, p. 350-357. DOI : 10.1016/j.mib.2010.03.001.

Production of biofuels and biochemicals: in need of an ORACLE

L. Miskovic; V. Hatzimanikatis 

Trends in Biotechnology. 2010. Vol. 28, num. 8, p. 391-397. DOI : 10.1016/j.tibtech.2010.05.003.

Closed-loop identication of MIMO systems: a new look at identifiability and experiment design

A. S. Bazanella; M. Gevers; L. Miskovic 

European Journal of Control. 2010. Vol. 16, num. 3, p. 228-239. DOI : 10.3166/EJC.16.228-239.

2009

Thermodynamic Analysis of Biodegradation Pathways

S. D. Finley; L. J. Broadbelt; V. Hatzimanikatis 

Biotechnology And Bioengineering. 2009. Vol. 103, p. 532-541. DOI : 10.1002/bit.22285.

Computational Framework for Predictive Biodegradation

S. D. Finley; L. J. Broadbelt; V. Hatzimanikatis 

Biotechnology And Bioengineering. 2009. Vol. 104, p. 1086-1097. DOI : 10.1002/bit.22489.

Identification and the information matrix: how to get just sufficiently rich?

M. Gevers; A. S. Bazanella; X. Bombois; L. Miskovic 

IEEE Transactions on Automatic Control. 2009. Vol. 54, num. 12, p. 2828-2840. DOI : 10.1109/TAC.2009.2034199.

2008

Group contribution method for thermodynamic analysis of complex metabolic networks

M. D. Jankowski; C. S. Henry; L. J. Broadbelt; V. Hatzimanikatis 

Biophysical Journal. 2008. Vol. 95, p. 1487-1499. DOI : 10.1529/biophysj.107.124784.

Effects of codon distributions and tRNA competition on protein translation

H. Zouridis; V. Hatzimanikatis 

Biophysical Journal. 2008. Vol. 95, p. 1018-1033. DOI : 10.1529/biophysj.107.126128.

Iterative minimization of H2 control performance criteria

A. Bazanella; M. Gevers; L. Miskovic; B. D. O. Anderson 

Automatica. 2008. Vol. 44, num. 10, p. 2549-2559. DOI : 10.1016/j.automatica.2008.03.014.

Closed-loop Identification of Multivariable Systems: With or Without Excitation of All References?

L. Miskovic; A. Karimi; D. Bonvin; M. Gevers 

Automatica. 2008. Vol. 44, num. 8, p. 2048-2056. DOI : 10.1016/j.automatica.2007.11.016.

2007

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

H. Zouridis; V. Hatzimanikatis 

Biophysical Journal. 2007. Vol. 92, num. 3, p. 717-730. DOI : 10.1529/biophysj.106.087825.

Thermodynamics-Based Metabolic Flux Analysis

C. S. Henry; L. J. Broadbelt; V. Hatzimanikatis 

Biophysical Journal. 2007. Vol. 92, num. 5, p. 1792-1805.

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

R. Thomas; C. J. Paredes; S. Mehrotra; V. Hatzimanikatis; E. T. Papoutsakis 

BMC Bioinformatics. 2007. Vol. 8, p. 228-239.

Correlation-Based Tuning of Decoupling Multivariable Controllers

L. Miskovic; A. Karimi; D. Bonvin; M. Gevers 

Automatica. 2007. Vol. 43, num. 9, p. 1481-1494. DOI : 10.1016/j.automatica.2007.02.006.

2006

Identification of multi-input systems: variance analysis and input design issues

M. Gevers; L. Miskovic; D. Bonvin; A. Karimi 

Automatica. 2006. Vol. 42, num. 4, p. 559-572. DOI : 10.1016/j.automatica.2005.12.017.

Analysis of the Maximum Theoretical Yield for the Synthesis of Erythromycin Precursors in Escherichia coli

J. Gonzalez-Lergier; L. J. Broadbelt; V. Hatzimanikatis 

Biotechnology and Bioengineering. 2006. Vol. 95, num. 4, p. 638-644. DOI : 10.1002/bit.20925.

Metabolic engineering under uncertainty. I: Framework development

L. Wang; V. Hatzimanikatis 

Metabolic Engineering. 2006. Vol. 8, num. 2, p. 133-141.

Metabolic engineering under uncertainty-II: Analysis of yeast metabolism

L. Wang; V. Hatzimanikatis 

Metabolic Engineering. 2006. Vol. 8, num. 2, p. 142-159.

Bistability explains threshold phenomena in protein aggregation both in vitro and in vivo

T. R. Rieger; R. I. Morimoto; V. Hatzimanikatis 

Biophysical Journal. 2006. Vol. 90, num. 3, p. 886-895.

An algorithmic framework for genome-wide modeling and analysis of translation networks

A. Mehra; V. Hatzimanikatis 

Biophysical Journal. 2006. Vol. 90, num. 4, p. 1136-1146.

Genome-scale thermodynamic analysis of Escherichia coli metabolism

C. S. Henry; M. D. Jankowski; L. J. Broadbelt; V. Hatzimanikatis 

Biophysical Journal. 2006. Vol. 90, num. 4, p. 1453-1461.

2005

Mathematical modeling of the eukaryotic heat-shock response: dynamics of the hsp70 promoter

T. R. Rieger; R. I. Morimoto; V. Hatzimanikatis 

Biophysical Journal. 2005. Vol. 88, num. 3, p. 1646-1658.

Preface

C. Maranas; V. Hatzimanikatis 

Computers & Chemical Engineering. 2005. Vol. 29, num. 3, p. 405-406. DOI : 10.1016/j.compchemeng.2004.08.008.

Exploring the diversity of complex metabolic networks

V. Hatzimanikatis; C. Li; J. A. Ionita; C. S. Henry; M. D. Jankowski et al. 

Bioinformatics. 2005. Vol. 21, num. 8, p. 1603-1609.

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

J. Gonzalez-Lergier; L. J. Broadbelt; V. Hatzimanikatis 

Journal of the American Chemical Society. 2005. Vol. 127, num. 27, p. 9930-9938. DOI : 10.1021/ja051586y.

2004

Metabolic control analysis under uncertainty: Framework development and case studies

L. Wang; I. Birol; V. Hatzimanikatis 

Biophysical Journal. 2004. Vol. 87, num. 6, p. 3750-3763.

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

R. Thomas; S. Mehrotra; E. T. Papoutsakis; V. Hatzimanikatis 

Bioinformatics. 2004. Vol. 20, num. 17, p. 3221-3235. DOI : 10.1093/bioinformatics/bth389.

Computational discovery of biochemical routes to specialty chemicals

C. Li; C. S. Henry; M. D. Jankowski; J. A. Ionita; V. Hatzimanikatis et al. 

Chemical Engineering Science. 2004. Vol. 59, num. 22-23, p. 5051-5060.

Metabolic networks: enzyme function and metabolite structure

V. Hatzimanikatis; C. Li; J. A. Ionita; L. J. Broadbelt 

Current Opinion in Structural Biology. 2004. Vol. 14, num. 3, p. 300-306. DOI : 10.1016/j.sbi.2004.04.004.

Iterative Correlation-Based Controller Tuning

A. Karimi; L. Miskovic; D. Bonvin 

International Journal of Adaptive Control and Signal Processing. 2004. Vol. 18, num. 8, p. 645-664. DOI : 10.1002/acs.825.

2003

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

A. Mehra; K. H. Lee; V. Hatzimanikatis 

Biotechnology and Bioengineering. 2003. Vol. 84, num. 7, p. 822-833. DOI : 10.1002/bit.10860.

Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli

P. S. Lee; L. B. Shaw; L. H. Choe; A. Mehra; V. Hatzimanikatis et al. 

Biotechnology and Bioengineering. 2003. Vol. 84, num. 7, p. 834-841.

Control of an Active Suspension System as a Benchmark for Design and Optimization of Restricted Complexity Controllers

I. D. Landau; A. Karimi; L. Miskovic; H. Prochazka 

European Journal of Control. 2003. Vol. 9, num. 1, p. 3-12.

Correlation-Based Tuning of a Restricted-Complexity Controller for an Active Suspension System

L. Miskovic; A. Karimi; D. Bonvin 

European Journal of Control. 2003. Vol. 9, num. 1, p. 77-83.

Iterative Correlation-Based Controller Tuning: Application to a Magnetic Suspension System

A. Karimi; L. Miskovic; D. Bonvin 

Control Engineering Practice. 2003. Vol. 11, num. 9, p. 1069-1078. DOI : 10.1016/S0967-0661(02)00191-0.

2002

Application of the minimum state error variance approach to nonlinear system control

L. Miskovic; Z. Djurovic; B. Kovacevic 

International Journal of Systems Science. 2002. Vol. 33, num. 5, p. 359-368. DOI : 10.1080/00207720210123706.

Jay Bailey as mentor-the students' perspective

K. F. Reardon; K. H. Lee; K. D. Wittrup; V. Hatzimanikatis 

Biotechnology and Bioengineering. 2002. Vol. 79, num. 5, p. 484-489. DOI : 10.1002/bit.10402.