Reconstructing organisms in silico: genome-scale models and their emerging applications
X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …
of published studies detailing its genes, its genome and the biochemical functions of its …
Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives
CA Vees, CS Neuendorf, S Pflügl - Journal of Industrial …, 2020 - academic.oup.com
The sustainable production of solvents from above ground carbon is highly desired. Several
clostridia naturally produce solvents and use a variety of renewable and waste-derived …
clostridia naturally produce solvents and use a variety of renewable and waste-derived …
[HTML][HTML] Heading in the right direction: thermodynamics-based network analysis and pathway engineering
M Ataman, V Hatzimanikatis - Current opinion in biotechnology, 2015 - Elsevier
Highlights•Reaction directionalities versus enzyme reversibility: role of thermodynamics.•
Assessment of methods for thermodynamics-based analysis of metabolic …
Assessment of methods for thermodynamics-based analysis of metabolic …
[HTML][HTML] A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories
AK Fisher, BG Freedman, DR Bevan… - Computational and …, 2014 - Elsevier
Microbial cell factories (MCFs) are of considerable interest to convert low value renewable
substrates to biofuels and high value chemicals. This review highlights the progress of …
substrates to biofuels and high value chemicals. This review highlights the progress of …
Systems-Level Modeling for CRISPR-Based Metabolic Engineering
RAL Cardiff, JM Carothers, JG Zalatan… - ACS Synthetic …, 2024 - ACS Publications
The CRISPR-Cas system has enabled the development of sophisticated, multigene
metabolic engineering programs through the use of guide RNA-directed activation or …
metabolic engineering programs through the use of guide RNA-directed activation or …
Towards a systems biology approach to understanding the lichen symbiosis: opportunities and challenges of implementing network modelling
Lichen associations, a classic model for successful and sustainable interactions between
micro-organisms, have been studied for many years. However, there are significant gaps in …
micro-organisms, have been studied for many years. However, there are significant gaps in …
Comparative analysis of high butanol tolerance and production in clostridia
Abstract 2016, was the 100 years anniversary from launching of the first industrial acetone-
butanol-ethanol (ABE) microbial production process. Despite this long period and also …
butanol-ethanol (ABE) microbial production process. Despite this long period and also …
A quantitative system-scale characterization of the metabolism of Clostridium acetobutylicum
M Yoo, G Bestel-Corre, C Croux, A Riviere… - MBio, 2015 - Am Soc Microbiol
Engineering industrial microorganisms for ambitious applications, for example, the
production of second-generation biofuels such as butanol, is impeded by a lack of …
production of second-generation biofuels such as butanol, is impeded by a lack of …
Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering
Metabolic pathways can be engineered to maximize the synthesis of various products of
interest. With the advent of computational systems biology, this endeavour is usually carried …
interest. With the advent of computational systems biology, this endeavour is usually carried …
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling
Metabolic modelling has entered a mature phase with dozens of methods and software
implementations available to the practitioner and the theoretician. It is not easy for a …
implementations available to the practitioner and the theoretician. It is not easy for a …