Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Y Chen, J Gustafsson, A Tafur Rangel, M Anton… - Nature …, 2024 - nature.com
Genome-scale metabolic models (GEMs) are computational representations that enable
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 …

Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum

J Niu, Z Mao, Y Mao, K Wu, Z Shi, Q Yuan, J Cai, H Ma - Biomolecules, 2022 - mdpi.com
The genome-scale metabolic model (GEM) is a powerful tool for interpreting and predicting
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 …

ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow

K Wu, Z Mao, Y Mao, J Niu, J Cai, Q Yuan, L Yun… - Microorganisms, 2023 - mdpi.com
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 …

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 …

Constraint-based reconstruction and analyses of metabolic models: open-source python tools and applications to cancer

RH Ng, JW Lee, P Baloni, C Diener, JR Heath… - Frontiers in …, 2022 - frontiersin.org
The influence of metabolism on signaling, epigenetic markers, and transcription is highly
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 …

[HTML][HTML] ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models

Z Mao, J Niu, J Zhao, Y Huang, K Wu, L Yun… - Synthetic and systems …, 2024 - Elsevier
Genome-scale metabolic models (GEMs) have been widely employed to predict
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 …