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Benefiting from big data in natural products: importance of preserving foundational skills and prioritizing data quality

NATURAL PRODUCT REPORTS (2021)

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Article Chemistry, Multidisciplinary

COCONUT online: Collection of Open Natural Products database

Maria Sorokina et al.

Summary: Natural products (NPs) are bioactive small molecules produced by living organisms, sparking global interest in NP research. Despite the existence of multiple NP databases, there is currently no resource that aggregates all known NPs in one place, which would greatly simplify research.

JOURNAL OF CHEMINFORMATICS (2021)

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Article Biology

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

Satria A. Kautsar et al.

Summary: BiG-SLiCE is a tool designed to cluster massive numbers of BGCs by representing them in Euclidean space to group BGCs into GCFs in a non-pairwise, near-linear fashion. It was used to analyze over 1.2 million BGCs collected from microbial genomes and metagenome-assembled genomes within 10 days. The tool offers a query mode to efficiently place newly sequenced BGCs into previously computed GCFs, along with a powerful output visualization engine for user-friendly data exploration.

GIGASCIENCE (2021)

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Article Plant Sciences

Interlaboratory Comparison of Untargeted Mass Spectrometry Data Uncovers Underlying Causes for Variability

Trevor N. Clark et al.

Summary: Despite challenges in comparing untargeted metabolomics data between laboratories, this study found that data sets with low feature overlap can still yield similar qualitative descriptions using PCA. Differences in fragmentation, charge state, and adduct formation in the ionization source were identified as major factors causing discrepancies in the data sets.

JOURNAL OF NATURAL PRODUCTS (2021)

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Article Multidisciplinary Sciences

An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes

Matthew T. Robey et al.

Summary: This study provides detailed annotation and analysis of fungal biosynthetic and chemical space, enabling genome mining and discovery of fungal natural products. The taxonomic landscape of fungal gene cluster families is largely species specific, revealing dramatic differences between fungal and bacterial biosynthetic logic and chemical space.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Chemistry, Medicinal

A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters

Allison S. Walker et al.

Summary: Research on natural products focuses on molecular structure, biosynthesis, and biological activity, with a lack of methods for predicting biological activity from genes. A machine learning bioinformatics method has been developed to predict antibiotic activity of natural products directly from biosynthetic gene cluster sequences, achieving accuracies up to 80% and identifying relevant enzymes and molecular features.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Review Biochemistry & Molecular Biology

The Science of Antibiotic Discovery

Kim Lewis

CELL (2020)

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Article Biochemical Research Methods

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Allegra T. Aron et al.

NATURE PROTOCOLS (2020)

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Article Chemistry, Medicinal

Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data

Saul H. Martinez-Trevino et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

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Article Multidisciplinary Sciences

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable surface

Uddhav K. Shigdel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Biochemical Research Methods

ReDU: a framework to find and reanalyze public mass spectrometry data

Alan K. Jarmusch et al.

NATURE METHODS (2020)

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Review Chemistry, Multidisciplinary

Linking genomics and metabolomics to chart specialized metabolic diversity

Justin J. J. van Der Hooft et al.

CHEMICAL SOCIETY REVIEWS (2020)

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Review Biochemistry & Molecular Biology

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

James B. McAlpine et al.

NATURAL PRODUCT REPORTS (2019)

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Article Chemistry, Multidisciplinary

Cadasides, Calcium-Dependent Acidic Lipopeptides from the Soil Metagenome That Are Active against Multidrug-Resistant Bacteria

Changsheng Wu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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Article Chemistry, Multidisciplinary

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

Jeffrey A. van Santen et al.

ACS CENTRAL SCIENCE (2019)

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Article Chemistry, Analytical

Hierarchical cluster analysis of technical replicates to identify interferents in untargeted mass spectrometry metabolomics

Lindsay K. Caesar et al.

ANALYTICA CHIMICA ACTA (2018)

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Article Microbiology

Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens

Bradley M. Hover et al.

NATURE MICROBIOLOGY (2018)

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Review Biochemistry & Molecular Biology

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

Ivana Blazenovic et al.

METABOLITES (2018)

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Article Chemistry, Analytical

Systems-Level Annotation of a 25 000 Features to Fewer than G Metabolomics Data Set Reduces 1000 Unique Metabolites

Nathaniel G. Mahieu et al.

ANALYTICAL CHEMISTRY (2017)

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Article Chemistry, Multidisciplinary

Artemisinin-A Gift from Traditional Chinese Medicine to the World (Nobel Lecture)

Youyou Tu

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)

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Article Chemistry, Analytical

RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data

C. D. Broeckling et al.

ANALYTICAL CHEMISTRY (2014)

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Review Chemistry, Analytical

Interferences and contaminants encountered in modern mass spectrometry

Bernd O. Keller et al.

ANALYTICA CHIMICA ACTA (2008)

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