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Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery

https://doi.org/10.1093/femsle/fnz142
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome‐Based Identification of a Plant‐Associated Marine Bacterium as a Rich Natural Product Source
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Dictionary of Natural Products
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Gifted microbes for genome mining and natural product discovery
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Urine-based metabolomic analysis of patients with Clostridium difficile infection: a pilot study
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A metabolomics guided exploration of marine natural product chemical space
inferredcites →https://doi.org/10.1016/j.biotechadv.2015.06.003openalex-snapshot
Elicitation of secondary metabolism in actinomycetes
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Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters
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Natural Product Proteomining, a Quantitative Proteomics Platform, Allows Rapid Discovery of Biosynthetic Gene Clusters for Different Classes of Natural Products
inferredcites →https://doi.org/10.1016/j.chembiol.2015.03.010openalex-snapshot
Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species
inferredcites →https://doi.org/10.1016/j.fgb.2010.06.003openalex-snapshot
SMURF: Genomic mapping of fungal secondary metabolite clusters
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Omics-based natural product discovery and the lexicon of genome mining
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Genome mining of Streptomyces olivaceus SCSIO T05: Discovery of olimycins A and B and assignment of absolute configurations
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Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols
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Ulleungdin, a Lasso Peptide with Cancer Cell Migration Inhibitory Activity Discovered by the Genome Mining Approach
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Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer
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Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations
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Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics
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Novel Methoxymethacrylate Natural Products Uncovered by Statistics-Based Mining of the Myxococcus fulvus Secondary Metabolome
inferredcites →https://doi.org/10.1021/cb500199hopenalex-snapshot
Automated Genome Mining of Ribosomal Peptide Natural Products
inferredcites →https://doi.org/10.1021/np500370copenalex-snapshot
NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery
inferredcites →https://doi.org/10.1038/nbt.3597openalex-snapshot
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
inferredcites →https://doi.org/10.1038/nchembio.1659openalex-snapshot
A roadmap for natural product discovery based on large-scale genomics and metabolomics
inferredcites →https://doi.org/10.1038/nchembio.1890openalex-snapshot
Minimum Information about a Biosynthetic Gene cluster
inferredcites →https://doi.org/10.1038/nchembio.2219openalex-snapshot
Dereplication of peptidic natural products through database search of mass spectra
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A new genome-mining tool redefines the lasso peptide biosynthetic landscape
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A mass spectrometry–guided genome mining approach for natural product peptidogenomics
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The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
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An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products
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Discovery of microbial natural products by activation of silent biosynthetic gene clusters
inferredcites →https://doi.org/10.1038/s41429-018-0105-4openalex-snapshot
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inferredcites →https://doi.org/10.1038/s41467-018-06082-8openalex-snapshot
Dereplication of microbial metabolites through database search of mass spectra
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Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome
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Native and engineered promoters in natural product discovery
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Heterologous expression of bacterial natural product biosynthetic pathways
inferredcites →https://doi.org/10.1039/c8sc02170hopenalex-snapshot
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inferredcites →https://doi.org/10.1039/c8sc03814gopenalex-snapshot
Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery
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PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin
inferredcites →https://doi.org/10.1073/pnas.1303471110openalex-snapshot
MS/MS networking guided analysis of molecule and gene cluster families
inferredcites →https://doi.org/10.1073/pnas.1614680114openalex-snapshot
Retrospective analysis of natural products provides insights for future discovery trends
inferredcites →https://doi.org/10.1073/pnas.1714381115openalex-snapshot
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality
inferredcites →https://doi.org/10.1093/bib/bbx020openalex-snapshot
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites
inferredcites →https://doi.org/10.1093/bioinformatics/btl366openalex-snapshot
An initial strategy for comparing proteins at the domain architecture level
inferredcites →https://doi.org/10.1093/bioinformatics/btx400openalex-snapshot
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
inferredcites →https://doi.org/10.1093/nar/gkr466openalex-snapshot
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
inferredcites →https://doi.org/10.1093/nar/gkv1012openalex-snapshot
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)
inferredcites →https://doi.org/10.1093/nar/gkx319openalex-snapshot
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
inferredcites →https://doi.org/10.1093/nar/gkx320openalex-snapshot
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes
inferredcites →https://doi.org/10.1101/gr.4126905openalex-snapshot
Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
inferredcites →https://doi.org/10.1111/j.1751-7915.2010.00219.xopenalex-snapshot
Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters
inferredcites →https://doi.org/10.1111/lam.12693openalex-snapshot
Isolation of a new antibacterial peptide actinokineosin fromActinokineospora spheciospongiaebased on genome mining
inferredcites →https://doi.org/10.1128/aem.00683-10openalex-snapshot
Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster
inferredcites →https://doi.org/10.1128/msystems.00028-15openalex-snapshot
An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria
inferredcites →https://doi.org/10.1371/journal.pcbi.1003822openalex-snapshot
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
inferredcites →https://doi.org/10.1371/journal.pone.0002551openalex-snapshot
Population Substructure and Control Selection in Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pone.0003252openalex-snapshot
Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment
inferredcites →https://doi.org/10.1371/journal.pone.0084028openalex-snapshot
MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data
inferredcites →https://doi.org/10.3389/fmicb.2015.00371openalex-snapshot
Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi
inferredcites →https://doi.org/10.3389/fmicb.2018.01660openalex-snapshot
CRISPR/Cas9-Based Editing of Streptomyces for Discovery, Characterization, and Production of Natural Products
inferredcites →https://doi.org/10.3389/fmicb.2018.03139openalex-snapshot
Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic
inferredcites →https://doi.org/10.3390/md16070244openalex-snapshot
Extending the “One Strain Many Compounds” (OSMAC) Principle to Marine Microorganisms
inferredcites →https://doi.org/10.3390/md17010072openalex-snapshot
Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore
inferredcites →https://doi.org/10.3390/md17020127openalex-snapshot
Identification of the Anti-Infective Aborycin Biosynthetic Gene Cluster from Deep-Sea-Derived Streptomyces sp. SCSIO ZS0098 Enables Production in a Heterologous Host

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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