From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

S Klamt, G Regensburger, MP Gerstl… - PLoS computational …, 2017 - journals.plos.org
Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic
pathways and have become an established tool for constraint-based modeling and …

Systems biology based metabolic engineering for non-natural chemicals

A Biz, S Proulx, Z Xu, K Siddartha, AM Indrayanti… - Biotechnology …, 2019 - Elsevier
Production of chemicals in microorganisms is no longer restricted to products arising from
native metabolic potential. In this review, we highlight the evolution of metabolic engineering …

[图书][B] An introduction to computational systems biology: systems-level modelling of cellular networks

K Raman - 2021 - taylorfrancis.com
This book delivers a comprehensive and insightful account of applying mathematical
modelling approaches to very large biological systems and networks—a fundamental aspect …

Green pathways: metabolic network analysis of plant systems

LM Dersch, V Beckers, C Wittmann - Metabolic engineering, 2016 - Elsevier
Metabolic engineering of plants with enhanced crop yield and value-added compositional
traits is particularly challenging as they probably exhibit the highest metabolic network …

Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes

J Chen, Y Huang, C Zhong - Biosystems, 2023 - Elsevier
The flux distribution in metabolic network can be decomposed as non-negative linear
combinations of elementary flux modes (EFMs). Identifying biologically relevant EFM …

A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

D Banerjee, D Parmar, N Bhattacharya… - BMC systems …, 2017 - Springer
Background The leading edge of the global problem of antibiotic resistance necessitates
novel therapeutic strategies. This study develops a novel systems biology driven approach …

Metabolic flux modeling of Gluconobacter oxydans enables improved production of bioleaching organic acids

JE Aston, VS Thompson, Y Fujita, DW Reed - Process Biochemistry, 2022 - Elsevier
Bioleaching with organic acids is an option for recovery of rare earth elements (REE) and or
other valuable metals from consumer or industrial wastes. Biohydrometallurgy can play an …

Which sets of elementary flux modes form thermodynamically feasible flux distributions?

MP Gerstl, C Jungreuthmayer, S Müller… - The FEBS …, 2016 - Wiley Online Library
Elementary flux modes (EFMs) are non‐decomposable steady‐state fluxes through
metabolic networks. Every possible flux through a network can be described as a …

In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products

AE Tafur Rangel, W Ríos, D Mejía, C Ojeda… - Frontiers in …, 2021 - frontiersin.org
Selecting appropriate metabolic engineering targets to build efficient cell factories
maximizing the bioconversion of industrial by-products to valuable compounds taking into …

A hierarchy of metabolite exchanges in metabolic models of microbial species and communities

YK Wedmark, JO Vik, O Øyås - PLOS Computational Biology, 2024 - journals.plos.org
The metabolic network of an organism can be analyzed as a constraint-based model. This
analysis can be biased, optimizing an objective such as growth rate, or unbiased, aiming to …