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2024

Rational strain design with minimal phenotype perturbation

B. Narayanan; D. R. Weilandt; M. Masid; L. Miskovic; V. Hatzimanikatis

Nature Communications. 2024-01-24. Vol. 15, num. 1, p. 723. DOI : 10.1038/s41467-024-44831-0.

2024

Rational strain design with minimal phenotype perturbation

2023

Metabolic interaction models recapitulate leaf microbiota ecology

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Dynamics of CLIMP-63 S-acylation control ER morphology

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

2022

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

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

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

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

2021

Editorial Overview: Mathematical modeling: It’s a matter of scale

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

The influence of the crowding assumptions in biofilm simulations

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

Development of Selective FXIa Inhibitors Based on Cyclic Peptides and Their Application for Safe Anticoagulation

Quantitative modeling of human metabolism: A call for a community effort

Constraint-based metabolic control analysis for rational strain engineering

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

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

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

An inverse method for mechanical characterization of heterogeneous diseased arteries using intravascular imaging

Offset-Free Economic MPC Based on Modifier Adaptation: Investigation of Several Gradient-Estimation Techniques

The solubility parameters of carbon dioxide and ionic liquids: Are they an enigma?

2020

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

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

MEMOTE for standardized genome-scale metabolic model testing

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

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

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

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

Impact of multi-micronutrient supplementation on lipidemia of children and adolescents

Real-time optimization of load sharing for gas compressors in the presence of uncertainty

Revisiting the concept of extents for chemical reaction systems using an enthalpy balance

Visible light plays a significant role during bacterial inactivation by the photo-fenton process, even at sub-critical light intensities

Modifier Adaptation as a Feedback Control Scheme

A note on efficient computation of privileged directions in modifier adaptation

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

2019

Statistical inference in ensemble modeling of cellular metabolism

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

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

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

110th Anniversary: From Solubility Parameters to Predictive Equation-of-State Modeling

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

Robust control of systems with sector nonlinearities via convex optimization: A data-driven approach

A data-driven approach to model-reference control with applications to particle accelerator power converters

Accelerated and adaptive modifier-adaptation schemes for the real-time optimization of uncertain systems

110th Anniversary: A Feature-Based Analysis of Static Real-Time Optimization Schemes

Dynamic Optimization of Reaction Systems via Exact Parsimonious Input Parameterization

Discovery and validation of temporal patterns involved in human brain ketometabolism in cerebral microdialysis fluids of traumatic brain injury patients

Distributed modifier-adaptation schemes for the real-time optimisation of uncertain interconnected systems

Education in Process Systems Engineering: Why it matters more than ever and how it can be structured

Incremental Parameter Estimation under Rank-Deficient Measurement Conditions

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

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

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

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

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

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

2018

Nanoparticle Conjugation of Human Papillomavirus 16 E7-long Peptides Enhances Therapeutic Vaccine Efficacy against Solid Tumors in Mice

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

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

2017

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

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

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

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

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

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

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

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