Microbial production of advanced biofuels

J Keasling, H Garcia Martin, TS Lee… - Nature Reviews …, 2021 - nature.com
Concerns over climate change have necessitated a rethinking of our transportation
infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced …

Identification of bioactive metabolites using activity metabolomics

MM Rinschen, J Ivanisevic, M Giera… - Nature reviews Molecular …, 2019 - nature.com
The metabolome, the collection of small-molecule chemical entities involved in metabolism,
has traditionally been studied with the aim of identifying biomarkers in the diagnosis and …

Machine learning-enabled retrobiosynthesis of molecules

T Yu, AG Boob, MJ Volk, X Liu, H Cui, H Zhao - Nature Catalysis, 2023 - nature.com
Retrobiosynthesis provides an effective and sustainable approach to producing functional
molecules. The past few decades have witnessed a rapid expansion of biosynthetic …

Review on natural products databases: where to find data in 2020

M Sorokina, C Steinbeck - Journal of cheminformatics, 2020 - Springer
Natural products (NPs) have been the centre of attention of the scientific community in the
last decencies and the interest around them continues to grow incessantly. As a …

MEMOTE for standardized genome-scale metabolic model testing

C Lieven, ME Beber, BG Olivier, FT Bergmann… - Nature …, 2020 - nature.com
To the Editor—Reconstructing metabolic reaction networks enables the development of
testable hypotheses of an organism's metabolism under different conditions 1. State-of-the …

Current status and applications of genome-scale metabolic models

C Gu, GB Kim, WJ Kim, HU Kim, SY Lee - Genome biology, 2019 - Springer
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …

Machine learning for metabolic engineering: A review

CE Lawson, JM Martí, T Radivojevic… - Metabolic …, 2021 - Elsevier
Abstract Machine learning provides researchers a unique opportunity to make metabolic
engineering more predictable. In this review, we offer an introduction to this discipline in …

BioModels—15 years of sharing computational models in life science

RS Malik-Sheriff, M Glont, TVN Nguyen… - Nucleic acids …, 2020 - academic.oup.com
Computational modelling has become increasingly common in life science research. To
provide a platform to support universal sharing, easy accessibility and model reproducibility …

The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions

R Jacoby, M Peukert, A Succurro, A Koprivova… - Frontiers in plant …, 2017 - frontiersin.org
In their natural environment, plants are part of a rich ecosystem including numerous and
diverse microorganisms in the soil. It has been long recognized that some of these microbes …

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

ME Beber, MG Gollub, D Mozaffari… - Nucleic acids …, 2022 - academic.oup.com
Abstract eQuilibrator (equilibrator. weizmann. ac. il) is a database of biochemical equilibrium
constants and Gibbs free energies, originally designed as a web-based interface. While the …