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 …

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 …

[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 …

[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 …

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 …

Towards a systems biology approach to understanding the lichen symbiosis: opportunities and challenges of implementing network modelling

H Nazem-Bokaee, EFY Hom, AC Warden… - Frontiers in …, 2021 - frontiersin.org
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 …

Comparative analysis of high butanol tolerance and production in clostridia

P Patakova, J Kolek, K Sedlar, P Koscova… - Biotechnology …, 2018 - Elsevier
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 …

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 …

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

F He, E Murabito, HV Westerhoff - Journal of The Royal …, 2016 - royalsocietypublishing.org
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 …

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling

S Vijayakumar, M Conway, P Lió… - Briefings in …, 2018 - academic.oup.com
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 …