V. Hatzimanikatis

Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration
20261 citationsauthor #5
Metabolic thermodynamics: pertinent reference state and energy potentials.
20260 citationsauthor #8
in silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity
20251 citationsauthor #3
Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production
20256 citationsauthor #9
Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
20253 citationsauthor #7
Multi-omics-driven kinetic modeling reveals metabolic adaptations and vulnerabilities in BRCA1-deficient ovarian cancer
20250 citationsauthor #3
Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss
20251 citationsauthor #13
The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions
20259 citationsauthor #3
Editorial Board: Biotechnology Journal 2/2024
20240 citationsauthor #28
Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites
20244 citationsauthor #11
Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infections
202418 citationsauthor #7
Thermodynamics determines the coupling between growth and byproduct production
20240 citationsauthor #2
Editorial Board: Biotechnology Journal 1/2024
20240 citationsauthor #26
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
202437 citationsauthor #4
Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking
20247 citationsauthor #3
Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression.
202415 citationsauthor #2
Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli
20246 citationsauthor #4
A constraint-based framework to reconstruct interaction networks in microbial communities
20242 citationsauthor #4
Host metabolic pathways essential for malaria and related hemoparasites in the infection of nucleated cells
20230 citationsauthor #11
Dynamics of CLIMP-63 S-acylation control ER morphology
202322 citationsauthor #12
Application of genome-scale models of metabolism and expression to the simulation and design of recombinant organisms
20231 citationsauthor #2
Editorial Board: Biotechnology Journal 9/2023
20230 citationsauthor #26
Editorial Board: Biotechnology Journal 12/2023
20230 citationsauthor #26
Editorial Board: Biotechnology Journal 8/2023
20230 citationsauthor #26
Linear Solvation–Energy Relationships (LSER) and Equation-of-State Thermodynamics: On the Extraction of Thermodynamic Information from the LSER Database
202311 citationsauthor #4
Transcriptional reprogramming by IL-2 variant generates metabolically active stem-like T cells
20233 citationsauthor #17
Enzyme promiscuous profiles for protein sequence and reaction annotation
20231 citationsauthor #4
From microbiome composition to functional engineering, one step at a time
202332 citationsauthor #10
Metabolic interaction models recapitulate leaf microbiota ecology
2023121 citationsauthor #7
Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations
202324 citationsauthor #3
Editorial Board: Biotechnology Journal 10/2023
20230 citationsauthor #26
Editorial Board: Biotechnology Journal 11/2023
20230 citationsauthor #26
Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks
202260 citationsauthor #5
Optimal enzyme utilization suggests concentrations and thermodynamics favor condition-specific saturations and binding mechanisms
20220 citationsauthor #3
Computational tools and resources for designing new pathways to small molecules.
202223 citationsauthor #3
NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions
20221 citationsauthor #9
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
202215 citationsauthor #7
Rational strain design with minimal phenotype perturbation
202215 citationsauthor #5
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
202213 citationsauthor #9
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx
202235 citationsauthor #5
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression
202229 citationsauthor #18
Generative Adversarial Networks for Dynamical Studies of Metabolism
20220 citationsauthor #5
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
202123 citationsauthor #2
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism
202110 citationsauthor #6
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli
20216 citationsauthor #3
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives
202156 citationsauthor #4
PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
20216 citationsauthor #2
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics
202173 citationsauthor #6
Pathway Design
20210 citationsauthor #3
Author response: NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism
20210 citationsauthor #6
ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds
202113 citationsauthor #3
Editorial Overview: Mathematical modeling: It's a matter of scale
20210 citationsauthor #2
The solubility parameters of carbon dioxide and ionic liquids: Are they an enigma?
202115 citationsauthor #2
The influence of the crowding assumptions in biofilm simulations
20217 citationsauthor #2
ATLASx: a computational map for the exploration of biochemical space
20218 citationsauthor #5
Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression
20213 citationsauthor #18
CHAPTER 10. Solvation Gibbs Energy: The Equation of State Approach
20213 citationsauthor #3
Quantitative modeling of human metabolism: A call for a community effort
20214 citationsauthor #2
Thermodynamics of Metabolic Pathways
20214 citationsauthor #3
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
202089 citationsauthor #2
Database for drug metabolism and comparisons, NICEdrug.ch, aids discovery and design
20200 citationsauthor #6
redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast.
20207 citationsauthor #2
Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism.
202099 citationsauthor #10
Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
20202 citationsauthor #3
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
20208 citationsauthor #20
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
202035 citationsauthor #3
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate–product pairs
202024 citationsauthor #2
Constraint-based metabolic control analysis for rational strain engineering
202021 citationsauthor #5
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
202043 citationsauthor #2
Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
20200 citationsauthor #20
MEMOTE for standardized genome-scale metabolic model testing
2020408 citationsauthor #20
Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power
202038 citationsauthor #5
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
20200 citationsauthor #20
Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
202044 citationsauthor #2
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
20192 citationsauthor #2
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
201945 citationsauthor #3
Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
2019120 citationsauthor #20
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
201923 citationsauthor #4
Large-scale kinetic metabolic models of Pseudomonas putida for a consistent design of metabolic engineering strategies
20191 citationsauthor #3
Dynamic Radiolabeling of S-Palmitoylated Proteins.
20193 citationsauthor #3
Impact of iron reduction on the metabolism of Clostridium acetobutylicum
201953 citationsauthor #4
110th Anniversary: From Solubility Parameters to Predictive Equation-of-State Modeling
20199 citationsauthor #3
Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites
201978 citationsauthor #5
TEX-FBA: A constraint-based method for integrating gene expression, thermodynamics, and metabolomics data into genome-scale metabolic models
201917 citationsauthor #4
Statistical inference in ensemble modeling of cellular metabolism
201914 citationsauthor #3
The effects of model complexity and size on metabolic flux distribution and control. Case study in E. coli
20193 citationsauthor #3
Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks
201919 citationsauthor #4
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
201892 citationsauthor #6
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
201811 citationsauthor #2
Assigning enzyme sequences to orphan and novel reactions using knowledge of substrate reactive sites
20180 citationsauthor #5
Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
201835 citationsauthor #5
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
201853 citationsauthor #20
Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.
20180 citationsauthor #3
Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism
201825 citationsauthor #2
Integrating metabolic networks into an individual based model of bacterial life in soil
20181 citationsauthor #3
Model Classification for Uncertainty Reduction in Biochemical Kinetic Models
20181 citationsauthor #4
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
201872 citationsauthor #3
Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations
20180 citationsauthor #3
The architecture of the endoplasmic reticulum is regulated by the reversible lipid modification of the shaping protein CLIMP-63
20183 citationsauthor #11
TOWARD THE IDENTIFICATION OF NEW CANCER THERAPY TARGETS USING METABOLIC MODELING IN A HUMAN GENOME SCALE
20170 citationsauthor #4

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