In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

P Maia, M Rocha, I Rocha - Microbiology and Molecular Biology …, 2016 - Am Soc Microbiol
Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …

Metabolic engineering for enhancing microbial biosynthesis of advanced biofuels

M Das, P Patra, A Ghosh - Renewable and Sustainable Energy Reviews, 2020 - Elsevier
Increasing global energy demand and environmental concerns associated with petroleum
have raised interest in biofuels for reducing dependency on crude oil and promote carbon …

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms

Y Toya, H Shimizu - Biotechnology advances, 2013 - Elsevier
Rational engineering of metabolism is important for bio-production using microorganisms.
Metabolic design based on in silico simulations and experimental validation of the metabolic …

Genome-scale modeling for metabolic engineering

E Simeonidis, ND Price - Journal of Industrial Microbiology and …, 2015 - academic.oup.com
We focus on the application of constraint-based methodologies and, more specifically, flux
balance analysis in the field of metabolic engineering, and enumerate recent developments …

A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae

P Branduardi, V Longo, NM Berterame, G Rossi… - Biotechnology for …, 2013 - Springer
Background The sustainable production of biofuels remains one of the major issues of the
upcoming years. Among the number of most desirable molecules to be produced, butanol …

Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli

K Tokuyama, S Ohno, K Yoshikawa, T Hirasawa… - Microbial cell …, 2014 - Springer
Abstract Background 3-hydroxypropionic acid (3HP) is an important chemical precursor for
the production of bioplastics. Microbial production of 3HP from glycerol has previously been …

FastPros: screening of reaction knockout strategies for metabolic engineering

S Ohno, H Shimizu, C Furusawa - Bioinformatics, 2014 - academic.oup.com
Motivation: Although constraint-based flux analysis of knockout strains has facilitated the
production of desirable metabolites in microbes, current screening methods have placed a …

Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain

K Tokuyama, Y Toya, T Horinouchi… - Biotechnology and …, 2018 - Wiley Online Library
Gene deletion strategies using flux balance analysis (FBA) have improved the growth‐
coupled production of various compounds. However, the productivities were often below the …

Microbial n‐butanol production from Clostridia to non‐Clostridial hosts

P Branduardi, F De Ferra, V Longo… - Engineering in Life …, 2014 - Wiley Online Library
In the context of the global objective of shifting from petroleum to a biomass‐based
economy, the research on fermentative strategies to produce alternative biofuels and …

Recent advances in metabolic engineering–integration of in silico design and experimental analysis of metabolic pathways

H Shimizu, Y Toya - Journal of bioscience and bioengineering, 2021 - Elsevier
Microorganisms are widely used to produce valuable compounds. Because thousands of
metabolic reactions occur simultaneously and many metabolic reactions are related to target …