Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
Madeleine Ernst
Kyo Bin Kang
Andrés Mauricio Caraballo-Rodríguez
Louis Felix Nothias
Joe Wandy
Christopher Chen
Mingxun Wang
Simon Rogers
Marnix H. Medema
Pieter C. Dorrestein
Justin J.J. van der Hooft
Metabolites, 2019
Kyo Bin Kang
Kang Kyo Bin
ORCID: 0000-0003-3290-1017
Email: kbkang@sookmyung.ac.kr
Prediction of tyrosinase inhibitory activities of Morus alba root bark extracts from HPLC fingerprints
10.1016/j.microc.2013.08.012
Anti-Influenza Activity of Betulinic Acid from Zizyphus jujuba on Influenza A/PR/8 Virus
10.4062/biomolther.2015.019
Jubanines F–J, cyclopeptide alkaloids from the roots of Ziziphus jujuba
10.1016/j.phytochem.2015.09.001
Identification of ginsenoside markers from dry purified extract of Panax ginseng by a dereplication approach and UPLC–QTOF/MS analysis
10.1016/j.jpba.2015.02.034
Antiplasmodial activity, cytotoxicity and structure-activity relationship study of cyclopeptide alkaloids
10.3390/molecules22020224
Catechin-Bound Ceanothane-Type Triterpenoid Derivatives from the Roots of Zizyphus jujuba
10.1021/acs.jnatprod.6b01103
Ceanothane- and lupane-type triterpene esters from the roots of Hovenia dulcis and their antiproliferative activity on HSC-T6 cells
10.1016/j.phytochem.2017.06.014
Cytotoxic Ceanothane- and Lupane-Type Triterpenoids from the Roots of Ziziphus jujuba
10.1021/acs.jnatprod.6b00525
UHPLC-ESI-qTOF-MS analysis of cyclopeptide alkaloids in the seeds of Ziziphus jujuba var. Spinosa
10.5478/MSL.2016.7.2.45
Acylphloroglucinolated Catechin and Phenylethyl Isocoumarin Derivatives from Agrimonia pilosa
10.1021/acs.jnatprod.6b00566
Ginsenoside 20(S)-Rh2 exerts anti-cancer activity through targeting IL-6-induced JAK2/STAT3 pathway in human colorectal cancer cells
10.1016/j.jep.2016.08.039
Combined Application of UHPLC-QTOF/MS, HPLC-ELSD and 1H–NMR Spectroscopy for Quality Assessment of DA-9801, A Standardised Dioscorea Extract
10.1002/pca.2659
Argininosecologanin, a secoiridoid-derived guanidine alkaloid from the roots of Lonicera insularis
10.1080/14786419.2017.1361953
C-Methylated Flavonoid Glycosides from Pentarhizidium orientale Rhizomes and Their Inhibitory Effects on the H1N1 Influenza Virus
10.1021/acs.jnatprod.7b00677
Berchemiosides A–C, 2-Acetoxy-ω-phenylpentaene Fatty Acid Triglycosides from the Unripe Fruits of Berchemia berchemiifolia
10.1021/acs.jnatprod.7b00602
Rhamnellosides A and B, ω-phenylpentaene fatty acid amide diglycosides from the fruits of rhamnella franguloides
10.3390/molecules23040752
Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng
10.1038/s41598-018-30262-7
Genome and evolution of the shade-requiring medicinal herb Panax ginseng
10.1111/pbi.12926
Simultaneous Determination and Stability Test of Two Phthalic Anhydride Derivatives, Senkyunolide A and Z-Ligustilide, in the Water Extract of Cnidium Rhizome from Different Geographical Regions and Species Using HPLC-UVD Analysis
10.1002/bkcs.11471
Chemical and genomic diversity of six Lonicera species occurring in Korea
10.1016/j.phytochem.2018.07.012
Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication
10.1021/acs.jnatprod.8b00292
The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity
10.1080/23802359.2018.1502637
Classficiation of Bupleuri Radix according to Geographical Origins using Near Infrared Spectroscopy (NIRS) Combined with Supervised Pattern Recognition
10.20307/nps.2018.24.3.164
Multiple Targets of 3-Dehydroxyceanothetric Acid 2-Methyl Ester to Protect Against Cisplatin-Induced Cytotoxicity in Kidney Epithelial LLC-PK1 Cells
10.3390/molecules24050878
Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
10.1016/j.foodchem.2019.125290
Molecular Networking Reveals the Chemical Diversity of Selaginellin Derivatives, Natural Phosphodiesterase-4 Inhibitors from Selaginella tamariscina
10.1021/acs.jnatprod.9b00049
Identification and semi-synthesis of 3-O-protocatechuoylceanothic acid, a novel and natural GPR120 agonist †
10.3390/molecules24193487
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
10.1038/s41596-020-0317-5
Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
10.1016/j.phytochem.2020.112292
Unique triterpenoid of jujube root protects cisplatin-induced damage in kidney epithelial LLC-PK1 cells via autophagy regulation
10.3390/nu12030677
Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
10.3390/metabo9070144
Combined MS/MS-NMR Annotation Guided Discovery of Iris lactea var. chinensis Seed as a Source of Viral Neuraminidase Inhibitory Polyphenols
10.3390/molecules25153383
Feature-based molecular networking in the GNPS analysis environment
10.1038/s41592-020-0933-6
A Metabolic Choreography of Maize Plants Treated with a Humic Substance-Based Biostimulant under Normal and Starved Conditions
10.3390/metabo11060403
Chemical and Biological Profiles of Dendrobium in Two Different Species, Their Hybrid, and Gamma-Irradiated Mutant Lines of the Hybrid Based on LC-QToF MS and Cytotoxicity Analysis
10.3390/plants10071376
Simon Rogers
Rogers Simon
ORCID: 0000-0003-3578-4477
An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells
10.1104/pp.15.01607
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.
10.1093/bioinformatics/btv072
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.
10.1093/bioinformatics/btu370
Probabilistic assignment of formulas to mass peaks in metabolomics experiments.
10.1093/bioinformatics/btn642
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.
10.1093/bioinformatics/btn553
Bayesian model-based inference of transcription factor activity.
10.1186/1471-2105-8-S2-S2
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.
10.1098/rsif.2005.0093
A Bayesian regression approach to the inference of regulatory networks from gene expression data.
10.1093/bioinformatics/bti487
The latent process decomposition of cDNA microarray data sets.
10.1109/TCBB.2005.29
HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data
10.1101/074831
Topic modeling for untargeted substructure exploration in metabolomics
10.1073/pnas.1608041113
Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics
10.1104/pp.17.00170
Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales
10.1105/tpc.17.00694
Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts
10.1038/s41598-018-28810-2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1101/491506
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture
10.1104/pp.18.00217
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.1101/744227
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.3390/metabo9100219
Gestational-age-dependent development of the neonatal metabolome
10.1101/2020.03.27.20045534
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Predicting host taxonomic information from viral genomes: A comparison of feature representations
10.1371/journal.pcbi.1007894
Decomposing metabolite set activity levels with PALS
10.1101/2020.06.07.138974
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
matchms - processing and similarity evaluation of mass spectrometry data
10.1101/2020.08.06.239244
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1101/2020.08.11.245928
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification
10.1101/2020.08.19.255653
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
User guide to the red blood cell model (RCM), a multiplatform JAVA-based model of human red blood cell homeostasis
10.1101/2020.03.07.981779
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
10.1093/bioinformatics/btaa998
Comparative Metabologenomics Analysis of Polar Actinomycetes
10.3390/md19020103
Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724
Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits
10.1371/journal.pcbi.1008706
PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells
10.1371/journal.pcbi.1008496
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
10.1039/D1NP00023C
Using topic modeling to detect cellular crosstalk in scRNA-seq
10.1101/2021.07.26.453767
Justin van der Hooft
van der Hooft Justin
/ Justin J.J. van der Hooft
ORCID: 0000-0002-9340-5511
Structural elucidation of low abundant metabolites in complex sample matrices
10.1007/s11306-013-0519-8
Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit
10.1105/tpc.113.114231
Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea
10.1021/ac400861a
Substructure-based annotation of high-resolution multistage MSn spectral trees
10.1002/rcm.6364
Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts
10.1021/jf300297y
Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake
10.1021/ac3017339
Spectral trees as a robust annotation tool in LC-MS based metabolomics
10.1007/s11306-011-0363-7
Metabolite identification using automated comparison of high-resolution multistage mass spectral trees
10.1021/ac2034216
Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi
10.1002/jsfa.5522
A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR
10.1002/mrc.2833
Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell
10.1063/1.3530735
Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation
10.1021/ac102546x
Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae)
10.1016/j.bse.2009.05.003
Topic modeling for untargeted substructure exploration in metabolomics
10.1073/pnas.1608041113
Propagating annotations of molecular networks using in silico fragmentation
10.1371/journal.pcbi.1006089
Did a plant-herbivore arms race drive chemical diversity in Euphorbia?
10.1101/323014
Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.
10.5702/massspectrometry.S0033
Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health
10.3945/ajcn.113.058263
Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes
10.1111/tpj.13527
Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines
10.3389/fbioe.2015.00026
Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption
10.1021/pr5001253
In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine
10.1021/ac403875b
Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose
10.1007/s11306-018-1438-5
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1101/463620
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1101/491506
Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics
10.1021/acs.analchem.8b05112
Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages
10.1101/347716
Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings
https://doi.org/10.1016/j.mam.2017.11.002
Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy
10.1007/978-3-319-28275-6_6-2
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
10.1093/bioinformatics/btx582
A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats
https://doi.org/10.1016/j.freeradbiomed.2016.08.001
The food metabolome: a window over dietary exposure
10.3945/ajcn.113.076133
Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols
10.3945/ajcn.113.058958
Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics
10.1021/acs.analchem.7b01391
A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes
10.18174/FAIRdata2018.16286
Implementations of the chemical structural and compositional similarity metric in R and Python
10.1101/546150
Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites 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
The Metabolomics Society—Current State of the Membership and Future Directions
10.3390/metabo9050089
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli
10.3389/fmicb.2019.00252
Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.
10.3389/fpls.2019.00846
Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
10.3390/metabo9070144
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.3390/metabo9100219
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
10.1093/nar/gkz882
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
10.1016/j.foodchem.2019.125290
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Mass spectrometry searches using MASST
10.1038/s41587-019-0375-9
Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
10.1016/j.phytochem.2020.112292
Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication
10.1126/sciadv.aax6328
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
10.1038/s41596-020-0317-5
Decomposing metabolite set activity levels with PALS
10.1101/2020.06.07.138974
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking
10.1021/acs.orglett.0c02153
matchms - processing and similarity evaluation of mass spectrometry data
10.1101/2020.08.06.239244
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1101/2020.08.11.245928
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
ReDU: a framework to find and reanalyze public mass spectrometry data
10.1038/s41592-020-0916-7
Feature-based molecular networking in the GNPS analysis environment
10.1038/s41592-020-0933-6
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
10.1038/s41589-020-00677-3
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
10.1038/s41587-020-0700-3
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
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
10.1093/gigascience/giaa154
Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs
10.1371/journal.ppat.1008932
Comparative Metabologenomics Analysis of Polar Actinomycetes
10.3390/md19020103
Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
10.1101/2021.04.18.440324
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview
10.3390/metabo11070445
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
Louis-Felix NOTHIAS
NOTHIAS Louis-Felix
ORCID: 0000-0001-6711-6719
Jatrophane diterpenes as inhibitors of chikungunya virus replication: structure-activity relationship and discovery of a potent lead.
10.1021/np500271u
Antiviral Activity of Diterpene Esters on Chikungunya Virus and HIV Replication
10.1021/acs.jnatprod.5b00073
LC-MS2-Based dereplication of Euphorbia extracts with anti-Chikungunya virus activity
10.1016/j.fitote.2015.06.021
Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation
10.1021/acs.jnatprod.7b00737
Propagating annotations of molecular networks using in silico fragmentation
10.1371/journal.pcbi.1006089
Did a plant-herbivore arms race drive chemical diversity in Euphorbia?
10.1101/323014
Niche partitioning of a pathogenic microbiome driven by chemical gradients
10.1126/sciadv.aau1908
Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking
10.1038/s41598-019-39583-7
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Feature-based Molecular Networking in the GNPS Analysis Environment
10.1101/812404
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
10.1101/842740
Classes for the masses: Systematic classification of unknowns using fragmentation spectra
10.1101/2020.04.17.046672
Ion Identity Molecular Networking in the GNPS Environment
10.1101/2020.05.11.088948
Database-independent molecular formula annotation using Gibbs sampling through ZODIAC
10.1038/s42256-020-00234-6
Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC
10.1038/s42256-020-00259-x
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
10.1038/s41587-020-0700-3
Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale
10.1021/jasms.0c00240
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
10.1038/s41587-020-0740-8
Reply to: Examining microbe–metabolite correlations by linear methods
10.1038/s41592-020-01007-0
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
Mauricio Caraballo
Caraballo Mauricio
/ Mauricio Caraballo
/ Andres M Caraballo-Rodriguez
ORCID: 0000-0001-5499-2728
Amphotericin B as an inducer of griseofulvin-containing guttate in the endophytic fungus Xylaria cubensis FLe9
10.1007/s00049-017-0243-3
Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides
10.1038/s41598-017-05532-5
Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype
10.1021/acs.jnatprod.6b00870
Endophytic Actinobacteria from the Brazilian Medicinal PlantLychnophora ericoidesMart. and the Biological Potential of Their Secondary Metabolites
10.1002/cbdv.201500225
Protocol for Community‐created Public MS/MS Reference Spectra Within the Global Natural Products Social Molecular Networking Infrastructure
10.1002/rcm.8725
Mass spectrometry searches using MASST
10.1038/s41587-019-0375-9
Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau
10.1021/acs.jnatprod.9b01128
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
10.1016/j.foodchem.2019.125290
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
10.1038/s41587-019-0209-9
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization
10.1038/s41467-019-09944-x
Propagating annotations of molecular networks using in silico fragmentation
10.1371/journal.pcbi.1006089
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
10.1038/nbt.3597
Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales
10.1016/j.ddmod.2019.08.012
Chemical signaling involved in plant–microbe interactions
10.1039/c7cs00343a
A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products
10.1021/jacs.9b13786
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
10.1007/978-1-62703-122-6_2
Synthetic Biology in Streptomyces Bacteria
10.1016/b978-0-12-385075-1.00021-4
Computational approaches to natural product discovery
10.1038/nchembio.1884
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
10.1038/nrmicro2478
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
10.1371/journal.pcbi.1004016
Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
10.1016/j.febslet.2011.06.014
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
10.1371/journal.pone.0051511
The future of industrial antibiotic production: From random mutagenesis to synthetic biology
10.4161/bbug.2.4.16114
Metabolomics methods for the synthetic biology of secondary metabolism
10.1016/j.febslet.2012.02.008
Computational tools for the synthetic design of biochemical pathways
10.1038/nrmicro2717
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
10.1186/1471-2164-11-299
Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
10.1111/j.1751-7915.2010.00226.x
Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea
10.1111/j.1462-2920.2008.01724.x
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
10.1371/journal.pcbi.1003822
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
10.1093/nar/gkv437
Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice
10.1016/j.copbio.2013.03.006
Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block
10.1021/sb500368w
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers
10.1093/nar/gkt449
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
10.1093/nar/gkr466
The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways
10.1093/gbe/evq013
MS/MS networking guided analysis of molecule and gene cluster families
10.1073/pnas.1303471110
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
10.1093/molbev/mst025
Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii
10.1128/jb.02132-12
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
10.1093/nar/gkr323
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
10.1128/mmbr.00037-08
Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
10.1186/s12864-015-2154-4
Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66
10.1021/acschembio.5b00801
Computational strategies for genome-based natural product discovery and engineering in fungi
10.1016/j.fgb.2016.01.006
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
10.1093/nar/gkw960
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
10.1038/nmicrobiol.2016.197
Editorial: Synthetic biology and bioinformatics
10.1039/c6np90031c
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1093/nar/gkx305
Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus
10.1186/s12864-017-3966-1
Mining prokaryotes for antimicrobial compounds: from diversity to function
10.1093/femsre/fux014
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
10.1093/bib/bbx146
Standardization for natural product synthetic biology
10.1039/c6np00030d
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways
10.1039/c6np00035e
Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin
10.1128/genomea.00453-17
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
10.1093/bioinformatics/btx400
Collaborating with Undergraduates To Contribute to Biochemistry Community Resources
10.1021/acs.biochem.7b00872
Road MAPs to engineer host microbiomes.
10.1016/j.mib.2017.11.023
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.
10.1111/1462-2920.13927
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
10.1073/pnas.1705567114
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
10.1093/nar/gkx319
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.
10.1016/j.fgb.2016.01.012
Exploration and exploitation of the environment for novel specialized metabolites.
10.1016/j.copbio.2018.01.017
Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
10.1128/mSystems.00182-17
Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.
10.1016/j.chembiol.2018.02.008
HEx: A heterologous expression platform for the discovery of fungal natural products.
10.1126/sciadv.aar5459
luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria.
10.1128/msystems.00208-17
A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
10.1021/jacs.7b13292
Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.
10.3389/fmicb.2018.01158
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
Madeleine Ernst
Ernst Madeleine
ORCID: 0000-0001-9530-3837
A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry
10.1016/j.aca.2015.01.002
Mass spectrometry in plant metabolomics strategies: From analytical platforms to data acquisition and processing
10.1039/c3np70086k
Mass Spectrometry of flavonoid vicenin-2, based sunlight barriers in Lychnophora species
10.1038/srep04309
Global medicinal uses of Euphorbia L. (Euphorbiaceae)
10.1016/j.jep.2015.10.025
A phylogenetic road map to antimalarial Artemisia species.
10.1016/j.jep.2018.06.030
Using evolutionary tools to search for novel psychoactive plants
10.1017/S1479262116000344
Updates on the genus Euphorbia (Euphorbiaceae) in Santa Catarina, Brazil
0.11646/phytotaxa.298.3.2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
Implementations of the chemical structural and compositional similarity metric in R and Python
10.1101/546150
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
Feature-based Molecular Networking in the GNPS Analysis Environment
10.1101/812404
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
10.1101/750471
Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS
10.1101/2020.01.13.905091
Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS.
10.26434/chemrxiv.9333212.v1
Gestational-age-dependent development of the neonatal metabolome
10.1101/2020.03.27.20045534
Untargeted metabolomic study of autism in newborn screening samples: a pilot study
10.1101/2020.04.17.20069153
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Thapsigargins and induced chemical defence in Thapsia garganica
10.1007/s00049-020-00315-3
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
Discovery of Urinary Biomarkers of Seaweed Intake Using Untargeted LC–MS Metabolomics in a Three-Way Cross-Over Human Study
10.3390/metabo11010011
Combined Urinary Biomarkers to Assess Coffee Intake Using Untargeted Metabolomics: Discovery in Three Pilot Human Intervention Studies and Validation in Cross-Sectional Studies
10.1021/acs.jafc.1c01155
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
