BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
Victoria Pascal Andreu
Hannah E. Augustijn
Koen van den Berg
Justin J. J. van der Hooft
Michael A. Fischbach
Marnix H. Medema
Michael Fischbach
Fischbach Michael
ORCID: 0000-0003-3079-8247
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Prokaryotic gene clusters: A rich toolbox for synthetic biology
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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
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CRISPR-based functional genomics in human dendritic cells
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Eliciting a potent antitumor immune response by expressing tumor antigens in a skin commensal
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Victoria Pascal Andreu
Pascal Andreu Victoria
ORCID: 0000-0001-9609-9401
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Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota
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Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota
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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
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Justin van der Hooft
van der Hooft Justin
/ Justin J.J. van der Hooft
ORCID: 0000-0002-9340-5511
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Propagating annotations of molecular networks using in silico fragmentation
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In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine
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Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
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Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics
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Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages
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Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy
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A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats
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The food metabolome: a window over dietary exposure
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Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols
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Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics
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A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes
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Implementations of the chemical structural and compositional similarity metric in R and Python
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Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
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A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
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The Metabolomics Society—Current State of the Membership and Future Directions
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
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MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
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Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli
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Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.
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Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
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MIBiG 2.0: a repository for biosynthetic gene clusters of known function
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Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
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The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
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Mass spectrometry searches using MASST
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Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
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Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication
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Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
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Linking genomics and metabolomics to chart specialized metabolic diversity
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Reproducible molecular networking of untargeted mass spectrometry data using GNPS
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Decomposing metabolite set activity levels with PALS
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Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
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Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking
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matchms - processing and similarity evaluation of mass spectrometry data
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
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BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
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matchms - processing and similarity evaluation of mass spectrometry data.
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ReDU: a framework to find and reanalyze public mass spectrometry data
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Feature-based molecular networking in the GNPS analysis environment
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Rapid Development of Improved Data-dependent Acquisition Strategies
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Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
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Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
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The ant fungus garden acts as an external digestive system
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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
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Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs
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Comparative Metabologenomics Analysis of Polar Actinomycetes
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Ranking Metabolite Sets by Their Activity Levels
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
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Rapid Development of Improved Data-Dependent Acquisition Strategies
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MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
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Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
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Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview
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Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery
10.1128/mSystems.00726-21
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
antiSMASH
10.1007/978-1-4899-7478-5_703
Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters
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Synthetic Biology in Streptomyces Bacteria
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Computational approaches to natural product discovery
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Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
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A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
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MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
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The future of industrial antibiotic production: From random mutagenesis to synthetic biology
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Metabolomics methods for the synthetic biology of secondary metabolism
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Computational tools for the synthetic design of biochemical pathways
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A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
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Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
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Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea
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Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters
10.1016/j.cell.2014.06.034
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
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Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice
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Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block
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antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers
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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
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The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways
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MS/MS networking guided analysis of molecule and gene cluster families
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Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
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Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii
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NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
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Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
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Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
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Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66
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Computational strategies for genome-based natural product discovery and engineering in fungi
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The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
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Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
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Editorial: Synthetic biology and bioinformatics
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plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
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Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus
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Mining prokaryotes for antimicrobial compounds: from diversity to function
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Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
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Standardization for natural product synthetic biology
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Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways
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Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin
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SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
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Collaborating with Undergraduates To Contribute to Biochemistry Community Resources
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Road MAPs to engineer host microbiomes.
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Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.
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Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
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antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
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Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.
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Exploration and exploitation of the environment for novel specialized metabolites.
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Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
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Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.
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HEx: A heterologous expression platform for the discovery of fungal natural products.
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
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Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.
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Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.
10.1038/s41396-018-0186-x
Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH.
10.1007/978-1-4939-7874-8_15
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences
10.1186/s40793-018-0318-y
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters
10.1093/nar/gky1060
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1101/463620
Mining bacterial genomes to reveal secret synergy
10.1074/jbc.H118.006669
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
10.1038/s42003-019-0333-6
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
10.1186/s13104-019-4222-3
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
10.1093/nar/gkz310
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs
10.1101/gr.243477.118
Genome Mining Approaches to Bacterial Natural Product Discovery
10.1016/b978-0-12-409547-2.14627-x
Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines
10.1039/C9NP00021F
PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1101/083535
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.
10.3389/fpls.2019.00846
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
10.1126/science.aaw9285
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
10.1093/nar/gkz882
A metabolic pathway for bile acid dehydroxylation by the gut microbiome
10.1101/758557
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines
10.1101/669291
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology
10.1038/s41564-019-0588-1
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1101/856955
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae
10.1111/nph.16338
Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat
10.1098/rspb.2019.2527
Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota
10.1101/2020.03.06.976126
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
10.1101/2020.03.14.992123
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota
10.1099/mgen.0.000373
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
10.1093/nar/gkaa374
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products
10.1101/2020.05.19.104752
Ecology and genomics of Actinobacteria: new concepts for natural product discovery
10.1038/s41579-020-0379-y
The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-0993-2
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1074/jbc.RA120.013528
Microbial natural product databases: moving forward in the multi-omics era
10.1039/D0NP00053A
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01228-1
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
10.1128/mSystems.00267-20
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01271-y
BiG-FAM: the biosynthetic gene cluster families database
10.1093/nar/gkaa812
Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic assembly lines
10.1093/bioinformatics/btaa595
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes
10.1093/nar/gkaa978
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
10.1038/s41598-020-77723-6
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
10.1371/journal.pbio.3001026
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
10.1093/gigascience/giaa154
The year 2020 in natural product bioinformatics: an overview of the latest tools and databases
10.1039/D0NP00090F
Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis
10.1101/2021.02.11.430889
A systematic analysis of metabolic pathways in the human gut microbiota
10.1101/2021.02.25.432841
Omics-based strategies to discover novel classes of RiPP natural products
10.1016/j.copbio.2020.12.008
Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria
10.1038/s41467-021-21163-x
The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range
10.3389/fbioe.2021.623701
Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques
10.1101/2021.01.20.427441
Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes
10.3389/fmicb.2020.574053
A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo
10.21203/rs.3.rs-126949/v1
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
10.1016/j.chembiol.2020.11.009
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters
10.1101/2020.11.08.370601
antiSMASH 6.0: improving cluster detection and comparison capabilities
10.1093/nar/gkab335
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
10.1093/nar/gkab353
Mining genomes to illuminate the specialized chemistry of life
10.1038/s41576-021-00363-7
Dominant drivers of the human plasma metabolome
10.21203/rs.3.rs-688716/v1
A global survey of specialized metabolic diversity encoded in bacterial genomes
10.1101/2021.08.11.455920
cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters
10.1093/bioadv/vbab016
