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 …
NPClassifier: a deep neural network-based structural classification tool for natural products
Computational approaches such as genome and metabolome mining are becoming
essential to natural products (NPs) research. Consequently, a need exists for an automated …
essential to natural products (NPs) research. Consequently, a need exists for an automated …
Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools
NF de Jonge, K Mildau, D Meijer, JJR Louwen… - Metabolomics, 2022 - Springer
Background Untargeted metabolomics approaches based on mass spectrometry obtain
comprehensive profiles of complex biological samples. However, on average only 10% of …
comprehensive profiles of complex biological samples. However, on average only 10% of …
MS2Query: reliable and scalable MS2 mass spectra-based analogue search
NF de Jonge, JJR Louwen, E Chekmeneva… - Nature …, 2023 - nature.com
Metabolomics-driven discoveries of biological samples remain hampered by the grand
challenge of metabolite annotation and identification. Only few metabolites have an …
challenge of metabolite annotation and identification. Only few metabolites have an …
Recent advances in proteomics and metabolomics in plants
Over the past decade, systems biology and plant-omics have increasingly become the main
stream in plant biology research. New developments in mass spectrometry and …
stream in plant biology research. New developments in mass spectrometry and …
Machine learning-assisted structure annotation of natural products based on MS and NMR data
G Hu, M Qiu - Natural Product Reports, 2023 - pubs.rsc.org
Covering: up to March 2023Machine learning (ML) has emerged as a popular tool for
analyzing the structures of natural products (NPs). This review presents a summary of the …
analyzing the structures of natural products (NPs). This review presents a summary of the …
Metabolome-guided genome mining of RiPP natural products
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a
chemically diverse class of metabolites. Many RiPPs show potent biological activities that …
chemically diverse class of metabolites. Many RiPPs show potent biological activities that …
Comparison of cosine, modified cosine, and neutral loss based spectrum alignment for discovery of structurally related molecules
Spectrum alignment of tandem mass spectrometry (MS/MS) data using the modified cosine
similarity and subsequent visualization as molecular networks have been demonstrated to …
similarity and subsequent visualization as molecular networks have been demonstrated to …
Advancements in capturing and mining mass spectrometry data are transforming natural products research
Covering: 2016 up to 2021 Mass spectrometry (MS) is an essential technology in natural
products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent …
products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent …