Recurrent topics in mass spectrometry-based metabolomics and lipidomics—standardization, coverage, and throughput

E Rampler, YE Abiead, H Schoeny, M Rusz… - Analytical …, 2020 - ACS Publications
We have come a long way in the last years of develo** analytical strategies in
metabolomics. We have seen huge progress in tackling multiplatform measurement, data …

Integrative omics approaches for biosynthetic pathway discovery in plants

KS Singh, JJJ van der Hooft, SCM van Wees… - Natural product …, 2022 - pubs.rsc.org
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 …

Feature-based molecular networking in the GNPS analysis environment

LF Nothias, D Petras, R Schmid, K Dührkop, J Rainer… - Nature …, 2020 - nature.com
Molecular networking has become a key method to visualize and annotate the chemical
space in non-targeted mass spectrometry data. We present feature-based molecular …

NPClassifier: a deep neural network-based structural classification tool for natural products

HW Kim, M Wang, CA Leber, LF Nothias… - Journal of natural …, 2021 - ACS Publications
Computational approaches such as genome and metabolome mining are becoming
essential to natural products (NPs) research. Consequently, a need exists for an automated …

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

M Ludwig, LF Nothias, K Dührkop, I Koester… - Nature Machine …, 2020 - nature.com
The confident high-throughput identification of small molecules is one of the most
challenging tasks in mass spectrometry-based metabolomics. Annotating the molecular …

Deep learning meets metabolomics: a methodological perspective

P Sen, S Lamichhane, VB Mathema… - Briefings in …, 2021 - academic.oup.com
Deep learning (DL), an emerging area of investigation in the fields of machine learning and
artificial intelligence, has markedly advanced over the past years. DL techniques are being …

Anaerobic gut fungi are an untapped reservoir of natural products

CL Swift, KB Louie, BP Bowen, HM Olson… - Proceedings of the …, 2021 - pnas.org
Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the
herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and …

A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases

C Kmezik, S Mazurkewich, T Meents, LS McKee… - Journal of Biological …, 2021 - jbc.org
The gut microbiota plays a central role in human health by enzymatically degrading dietary
fiber and concomitantly excreting short chain fatty acids that are associated with manifold …

[HTML][HTML] Untargeted metabolomics revealed essential biochemical rearrangements towards combined heat and drought stress acclimatization in Pinus pinaster

C López-Hidalgo, L Lamelas, MJ Cañal… - Environmental and …, 2023 - Elsevier
Trees usually face simultaneous stresses and have evolved to deal with them naturally.
However, as a consequence of climate change, heat waves and drought stress have …

The LOTUS initiative for open natural products research: knowledge management through Wikidata

A Rutz, M Sorokina, J Galgonek, D Mietchen… - BioRxiv, 2021 - biorxiv.org
As contemporary bioinformatic and chemoinformatic capabilities are resha** natural
products research, major benefits could result from an open database of referenced …