Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
Genome-scale metabolic models (GEMs) are computational representations that enable
mathematical exploration of metabolic behaviors within cellular and environmental …
mathematical exploration of metabolic behaviors within cellular and environmental …
[HTML][HTML] Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints
EJ Kerkhoven - Current Opinion in Microbiology, 2022 - Elsevier
The concept of metabolic models with resource allocation constraints has been around for
over a decade and has clear advantages even when implementation is relatively …
over a decade and has clear advantages even when implementation is relatively …
Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
The genome-scale metabolic model (GEM) is a powerful tool for interpreting and predicting
cellular phenotypes under various environmental and genetic perturbations. However, GEM …
cellular phenotypes under various environmental and genetic perturbations. However, GEM …
[HTML][HTML] Model-driven insights into the effects of temperature on metabolism
P Wendering, Z Nikoloski - Biotechnology Advances, 2023 - Elsevier
Temperature affects cellular processes at different spatiotemporal scales, and identifying the
genetic and molecular mechanisms underlying temperature responses paves the way to …
genetic and molecular mechanisms underlying temperature responses paves the way to …
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
Genome-scale metabolic models (GEMs) play an important role in the phenotype prediction
of microorganisms, and their accuracy can be further improved by integrating other types of …
of microorganisms, and their accuracy can be further improved by integrating other types of …
Genome-scale metabolic network models for industrial microorganisms metabolic engineering: current advances and future prospects
Z Gong, J Chen, X Jiao, H Gong, D Pan, L Liu… - Biotechnology …, 2024 - Elsevier
The construction of high-performance microbial cell factories (MCFs) is the centerpiece of
biomanufacturing. However, the complex metabolic regulatory network of microorganisms …
biomanufacturing. However, the complex metabolic regulatory network of microorganisms …
Constraint-based reconstruction and analyses of metabolic models: open-source python tools and applications to cancer
The influence of metabolism on signaling, epigenetic markers, and transcription is highly
complex yet important for understanding cancer physiology. Despite the development of …
complex yet important for understanding cancer physiology. Despite the development of …
Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective
WL Schroeder, PF Suthers, TC Willis, EJ Mooney… - Metabolites, 2024 - mdpi.com
Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or
GEM) have had many applications in exploring phenotypes and guiding metabolic …
GEM) have had many applications in exploring phenotypes and guiding metabolic …
[HTML][HTML] ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models
Genome-scale metabolic models (GEMs) have been widely employed to predict
microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading …
microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading …
Co‐Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation …
B Xue, Y Liu, C Yang, H Liu, Q Yuan… - Advanced …, 2024 - Wiley Online Library
Synthetic consortia have emerged as a promising biosynthetic platform that offers new
opportunities for biosynthesis. Genome‐scale metabolic network models (GEMs) with …
opportunities for biosynthesis. Genome‐scale metabolic network models (GEMs) with …