List of works by Vassily Hatzimanikatis

A computational framework for integration of lipidomics data into metabolic pathways

scientific article

A computational framework for the design of optimal protein synthesis

scientific article published on 24 February 2012

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

scientific article published on 19 March 2021

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

scientific article

A genome-scale integration and analysis of Lactococcus lactis translation data

scientific article

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

scientific article (publication date: 2007)

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

scientific article

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.

scientific article

A model for protein translation: polysome self-organization leads to maximum protein synthesis rates.

scientific article published on 10 November 2006

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

scientific article

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

scientific article

A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor

scientific article (publication date: 2013)

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

scientific article published in 2022

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

scientific article published on 12 July 2016

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

scientific article

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

article by Vassily Hatzimanikatis et al published May 1996 in AIChE Journal

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

scientific article published on May 2016

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

scientific article published on 04 June 2020

Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli

scientific article published in November 2006

Assigning enzyme sequences to orphan and novel reactions using knowledge of substrate reactive sites

article published in 2017

Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

scientific article published on 23 July 2020

Biochemical engineering

article published in 2002

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

scientific article

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

scientific article

Computational discovery of biochemical routes to specialty chemicals

Computational framework for predictive biodegradation

scientific article

Constraining the flux space using thermodynamics and integration of metabolomics data

scientific article

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

scientific article published in 2019

DREAMS of metabolism

scientific article published on 19 August 2010

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

scientific article

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

scientific article published on 07 August 2018

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

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

scientific article published in June 2010

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

scientific article published on 14 October 2015

Dynamic Radiolabeling of S-Palmitoylated Proteins

scientific article published on 01 January 2019

Dynamical analysis of gene networks requires both mRNA and protein expression information.

scientific article published in October 1999

Editorial: metabolic modeling in biotechnology and medical research

scientific article

Effects of codon distributions and tRNA competition on protein translation

scientific article published on 21 March 2008

Efficient cleavage of aryl ether C-O linkages by Rh-Ni and Ru-Ni nanoscale catalysts operating in water

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

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

scientific article published on 13 May 2019

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

scientific article published on 25 March 2019

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

scientific article published on 23 March 2022

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

scientific article published on 7 August 2012

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

scientific article

Exploring the diversity of complex metabolic networks.

scientific article

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

scientific article published on 19 December 2011

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

scientific article published on 27 January 2020

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

scientific article published on 22 June 2013

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage

scientific article published on 01 November 2019

Genome-scale thermodynamic analysis of Escherichia coli metabolism

scientific article

Group contribution method for thermodynamic analysis of complex metabolic networks

scientific article published on August 2008

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

scientific article

Identification and dynamics of the human ZDHHC16-ZDHHC6 palmitoylation cascade.

scientific article

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

scientific article

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

scientific article published on 16 May 2019

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

scientific article

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

scientific article published in December 2003

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

scientific article

Integrating computational methods to retrofit enzymes to synthetic pathways.

scientific article published on 28 September 2011

Integrative approaches for signalling and metabolic networks

Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes

scientific article published in September 2002

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

scientific article published on 19 April 2019

Jay Bailey as mentor--the students' perspective.

scientific article

Kinetic models in industrial biotechnology - Improving cell factory performance

scientific article published on 16 April 2014

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

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

scientific article published on 26 October 2018

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

scientific article published on 28 February 2020

Large-scale kinetic metabolic models of Pseudomonas putida for a consistent design of metabolic engineering strategies

MCA has more to say.

scientific article published in October 1996

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

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

scientific article (publication date: 2011)

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

scientific article

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

scientific article published on 19 February 2017

Mechanistically consistent reduced models of synthetic gene networks.

scientific article published on May 2013

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

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

scientific article

Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli

scientific article

Metabolic control analysis under uncertainty: framework development and case studies

scientific article

Metabolic engineering under uncertainty--II: analysis of yeast metabolism

scientific article published on 18 January 2006

Metabolic engineering under uncertainty. I: framework development

scientific article published on 18 January 2006

Metabolic interaction models recapitulate leaf microbiota ecology

scientific article published on 06 July 2023

Metabolic networks: enzyme function and metabolite structure.

scientific article

Model Classification for Uncertainty Reduction in Biochemical Kinetic Models

article

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

scientific article

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

scientific article published on 19 June 2019

Modeling of uncertainties in biochemical reactions.

scientific article published in February 2011

Modelling molecular mechanisms within their cellular environment

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

scientific article published on 22 November 2016

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

scientific article published in April 2015

Network thermodynamics in the post-genomic era.

scientific article published on 06 April 2010

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

scientific article

Nonlinear metabolic control analysis.

scientific article published in January 1999

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

scientific article published on 25 June 2019

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

scientific article published on 18 June 2010

Proteomics: theoretical and experimental considerations.

scientific article published in May 1999

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

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

scientific article published on 24 February 2016

Rational strain design with minimal phenotype perturbation

scientific article published on 24 January 2024

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

scientific article published on August 1995

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

scientific article published on 29 November 2016

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

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

scientific article

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

scientific article published on 3 August 2017

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

scientific article published on 22 July 2021

Statistical inference in ensemble modeling of cellular metabolism

scientific article published on 09 December 2019

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

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

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

scientific article published in 2022

Systems biology

scientific article published on 15 July 2011

TEX-FBA: A constraint-based method for integrating gene expression, thermodynamics, and metabolomics data into genome-scale metabolic models

article

The AlkB monooxygenase of Pseudomonas oleovorans--synthesis, stability and level in recombinant Escherichia coli and the native host.

scientific article published in March 1997

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

scientific article published on 13 January 2020

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

scientific article published in 2021

The influence of the crowding assumptions in biofilm simulations

scientific article published on 22 July 2021

The origins of time-delay in template biopolymerization processes

scientific article

Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways.

scientific article published on July 2005

Thermodynamic analysis of biodegradation pathways

scientific article

Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks

scientific article

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.

scientific article published on 11 November 2016

Thermodynamics-based metabolic flux analysis

scientific article published on 15 December 2006

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

scientific article published on 20 August 2013

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

scientific article published on 15 January 2013

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

scientific article published on 20 August 2019

Updated ATLAS of Biochemistry with new metabolites and improved enzyme prediction power

scientific article published on 18 May 2020

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

scientific article

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

scientific article

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

scientific article published on 01 January 2019

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

scientific article published on 20 July 2017

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