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 …

State-of the-art constraint-based modeling of microbial metabolism: from basics to context-specific models with a focus on methanotrophs

MA Kulyashov, SK Kolmykov, TM Khlebodarova… - Microorganisms, 2023 - mdpi.com
Methanotrophy is the ability of an organism to capture and utilize the greenhouse gas,
methane, as a source of energy-rich carbon. Over the years, significant progress has been …

[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 …

[HTML][HTML] Reconstruction and metabolic profiling of the genome-scale metabolic network model of pseudomonas stutzeri a1501

Q Yuan, F Wei, X Deng, A Li, Z Shi, Z Mao, F Li… - Synthetic and Systems …, 2023 - Elsevier
Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the
gram-negative bacterial group. As a prominent strain in the fields of agriculture and …

Systems metabolic engineering of Corynebacterium glutamicum to assimilate formic acid for biomass accumulation and succinic acid production

K Li, X Zhang, C Li, YC Liang, XQ Zhao, CG Liu… - Bioresource …, 2024 - Elsevier
Formate as an ideal mediator between the physicochemical and biological realms can be
obtained from electrochemical reduction of CO 2 and used to produce bio-chemicals. Yet …

Targeting the Bottlenecks in Levan Biosynthesis Pathway in Bacillus subtilis and Strain Optimization by Computational Modeling and Omics Integration

A Immanuel, RM Yennamalli… - OMICS: A Journal of …, 2024 - liebertpub.com
Levan is a fructan polymer with many industrial applications such as the formulation of
hydrogels, drug delivery, and wound healing, among others. To this end, metabolic systems …

Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design

F Wei, J Cai, Y Mao, R Wang, H Li, Z Mao… - Advanced …, 2024 - Wiley Online Library
Constructing efficient cell factories requires the rational design of metabolic pathways, yet
quantitatively predicting the potential pathway for breaking stoichiometric yield limit in hosts …

[HTML][HTML] Deciphering and designing microbial communities by genome-scale metabolic modelling

S Wu, Z Qu, D Chen, H Wu, Q Caiyin, J Qiao - Computational and Structural …, 2024 - Elsevier
Microbial communities are shaped by the complex interactions among organisms and the
environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the …

[HTML][HTML] CPhaMAS: An online platform for pharmacokinetic data analysis based on optimized parameter fitting algorithm

Y Kuang, D Cao, Y Zuo, J Yuan, F Lu, Y Zou… - Computer Methods and …, 2024 - Elsevier
Background and objective Clinical pharmacological modeling and statistical analysis
software is an essential basic tool for drug development and personalized drug therapy. The …

Unlocking the formate utilization of wild‐type Yarrowia lipolytica through adaptive laboratory evolution

Q Chen, Y Chen, Z Hou, Y Ma, J Huang… - Biotechnology …, 2024 - Wiley Online Library
Synthetic biology is contributing to the advancement of the global net‐negative carbon
economy, with emphasis on formate as a member of the one‐carbon substrate garnering …