Mass spectrometry-based metabolomics in microbiome investigations
A Bauermeister, H Mannochio-Russo… - Nature Reviews …, 2022 - nature.com
Microbiotas are a malleable part of ecosystems, including the human ecosystem.
Microorganisms affect not only the chemistry of their specific niche, such as the human gut …
Microorganisms affect not only the chemistry of their specific niche, such as the human gut …
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data
Background: Global or untargeted metabolomics is widely used to comprehensively
investigate metabolic profiles under various pathophysiological conditions such as …
investigate metabolic profiles under various pathophysiological conditions such as …
Advances in decomposing complex metabolite mixtures using substructure-and network-based computational metabolomics approaches
Covering: up to the end of 2020 Recently introduced computational metabolome mining
tools have started to positively impact the chemical and biological interpretation of …
tools have started to positively impact the chemical and biological interpretation of …
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Over-representation analysis (ORA) is one of the commonest pathway analysis approaches
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
used for the functional interpretation of metabolomics datasets. Despite the widespread use …
Metabolomics and complementary techniques to investigate the plant phytochemical cosmos
Covering: up to 2021 Plants and their associated microbial communities are known to
produce millions of metabolites, a majority of which are still not characterized and are …
produce millions of metabolites, a majority of which are still not characterized and are …
Integrative omics approaches for biosynthetic pathway discovery in plants
Covering: up to 2022 With the emergence of large amounts of omics data, computational
approaches for the identification of plant natural product biosynthetic pathways and their …
approaches for the identification of plant natural product biosynthetic pathways and their …
Recent advances in mass spectrometry-based computational metabolomics
The computational metabolomics field brings together computer scientists, bioinformaticians,
chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide …
chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide …
Single sample pathway analysis in metabolomics: performance evaluation and application
C Wieder, RPJ Lai, TMD Ebbels - BMC bioinformatics, 2022 - Springer
Background Single sample pathway analysis (ssPA) transforms molecular level omics data
to the pathway level, enabling the discovery of patient-specific pathway signatures …
to the pathway level, enabling the discovery of patient-specific pathway signatures …
Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess
optimisation. However, in most cases, only the biosynthetic pathway directed to product …
optimisation. However, in most cases, only the biosynthetic pathway directed to product …
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
V Pascal Andreu, HE Augustijn, K van den Berg… - Msystems, 2021 - Am Soc Microbiol
Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites
play key roles in shaping microbial ecosystems and driving microbiome-associated …
play key roles in shaping microbial ecosystems and driving microbiome-associated …