Genome-scale metabolic network models: From first-generation to next-generation

C Ye, X Wei, T Shi, X Sun, N Xu, C Gao… - Applied microbiology and …, 2022 - Springer
Over the last two decades, thousands of genome-scale metabolic network models (GSMMs)
have been constructed. These GSMMs have been widely applied in various fields, ranging …

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

I Otero-Muras, P Carbonell - Metabolic Engineering, 2021 - Elsevier
Metabolic engineering involves the engineering and optimization of processes from single-
cell to fermentation in order to increase production of valuable chemicals for health, food …

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

M Ataman, DF Hernandez Gardiol… - PLoS computational …, 2017 - journals.plos.org
Genome-scale metabolic reconstructions have proven to be valuable resources in
enhancing our understanding of metabolic networks as they encapsulate all known …

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

HV Dinh, PF Suthers, SHJ Chan, Y Shen, T Xiao… - Metabolic Engineering …, 2019 - Elsevier
Rhodosporidium toruloides is a red, basidiomycetes yeast that can accumulate a large
amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic …

Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana

A Küken, K Gennermann, Z Nikoloski - The Plant Journal, 2020 - Wiley Online Library
Availability of plant‐specific enzyme kinetic data is scarce, limiting the predictive power of
metabolic models and precluding identification of genetic factors of enzyme properties …

Active and machine learning-based approaches to rapidly enhance microbial chemical production

P Kumar, PA Adamczyk, X Zhang, RB Andrade… - Metabolic …, 2021 - Elsevier
In order to make renewable fuels and chemicals from microbes, new methods are required
to engineer microbes more intelligently. Computational approaches, to engineer strains for …

Learning metabolic dynamics from irregular observations by Bidirectional Time-Series State Transfer Network

S Xu, T Xu, Y Yang, X Chen - Msystems, 2024 - journals.asm.org
Modeling microbial metabolic dynamics is important for the rational optimization of both
biosynthetic systems and industrial processes to facilitate green and efficient …

Frontiers and opportunities in bioenergy crop microbiome research networks

TIBRCMWCA Howe, G Bonito, MY Chou… - Phytobiomes …, 2022 - Am Phytopath Society
Researchers from across the four United States Department of Energy Bioenergy Research
Centers (BRCs) engaged in a microbiome workshop that focused on identifying challenges …

Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine

AR Zomorrodi, C Hemez, P Arranz-Gibert, T Wu… - Iscience, 2022 - cell.com
Introducing heterologous pathways into host cells constitutes a promising strategy for
synthesizing nonstandard amino acids (nsAAs) to enable the production of proteins with …

Dissecting metabolic flux in C4 plants: experimental and theoretical approaches

MM Islam, A Al-Siyabi, R Saha, T Obata - Phytochemistry Reviews, 2018 - Springer
C 4 photosynthesis is the carbon fixation pathway in specific plant species, so called C 4
plants including maize, sorghum and sugarcane. It is characterized by the carboxylation …