From microbiome composition to functional engineering, one step at a time

SD Burz, S Causevic, A Dal Co… - Microbiology and …, 2023 - Am Soc Microbiol
Communities of microorganisms (microbiota) are present in all habitats on Earth and are
relevant for agriculture, health, and climate. Deciphering the mechanisms that determine …

[HTML][HTML] Kinetic models in industrial biotechnology–improving cell factory performance

J Almquist, M Cvijovic, V Hatzimanikatis, J Nielsen… - Metabolic …, 2014 - Elsevier
An increasing number of industrial bioprocesses capitalize on living cells by using them as
cell factories that convert sugars into chemicals. These processes range from the production …

[HTML][HTML] Lipidomics: new tools and applications

MR Wenk - Cell, 2010 - cell.com
Once viewed simply as a reservoir for carbon storage, lipids are no longer cast as
bystanders in the drama of biological systems. The emerging field of lipidomics is driven by …

Pathway thermodynamics highlights kinetic obstacles in central metabolism

E Noor, A Bar-Even, A Flamholz, E Reznik… - PLoS computational …, 2014 - journals.plos.org
In metabolism research, thermodynamics is usually used to determine the directionality of a
reaction or the feasibility of a pathway. However, the relationship between thermodynamic …

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

PA Saa, LK Nielsen - Biotechnology advances, 2017 - Elsevier
Kinetic models are critical to predict the dynamic behaviour of metabolic networks.
Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting …

Simulated design–build–test–learn cycles for consistent comparison of machine learning methods in metabolic engineering

P van Lent, J Schmitz, T Abeel - ACS Synthetic Biology, 2023 - ACS Publications
Combinatorial pathway optimization is an important tool in metabolic flux optimization.
Simultaneous optimization of a large number of pathway genes often leads to combinatorial …

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

A Khodayari, AR Zomorrodi, JC Liao, CD Maranas - Metabolic engineering, 2014 - Elsevier
In contrast to stoichiometric-based models, the development of large-scale kinetic models of
metabolism has been hindered by the challenge of identifying kinetic parameter values and …

Reconstructing kinetic models for dynamical studies of metabolism using generative adversarial networks

S Choudhury, M Moret, P Salvy, D Weilandt… - Nature Machine …, 2022 - nature.com
Kinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme
levels through mechanistic relations, rendering them essential for understanding, predicting …

Cofactor engineering for more efficient production of chemicals and biofuels

M Wang, B Chen, Y Fang, T Tan - Biotechnology advances, 2017 - Elsevier
Cofactors are involved in numerous intracellular reactions and critically influence redox
balance and cellular metabolism. Cofactor engineering can support and promote the …

Strategies for microbial synthesis of high-value phytochemicals

S Li, Y Li, CD Smolke - Nature chemistry, 2018 - nature.com
Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit
low abundance in nature. Recent demonstrations of industrial-scale production of …