Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
Andrés Mauricio Caraballo-Rodríguez Sara P. Puckett Kathleen E. Kyle Daniel Petras Ricardo da Silva Louis-Félix Nothias Madeleine Ernst Justin J. J. van der Hooft Anupriya Tripathi Mingxun Wang Marcy J. Balunas Jonathan L. Klassen Pieter C. Dorrestein Christopher W. Schadt
mSystems, 2021-8-31
Mingxun Wang
Wang Mingxun / Ming
ORCID: 0000-0001-7647-6097
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking 10.1038/nbt.3597
Detection of Ovarian Cancer Using Samples Sourced from the Vaginal Microenvironment 10.1101/597740
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471
Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure 10.1101/804401
Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure 10.1002/rcm.8725
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service 10.1101/2020.05.09.086066
Ion Identity Molecular Networking in the GNPS Environment 10.1101/2020.05.11.088948
ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7
The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment 10.1038/s41467-021-23953-9
Quick-start infrastructure for untargeted metabolomics analysis in GNPS 10.1038/s42255-021-00429-0
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21
A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals. 10.21203/rs.3.rs-820302/v1
Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors 10.1101/2021.09.03.458897
Ricardo da Silva
da Silva Ricardo
ORCID: 0000-0001-6378-0479
Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter 10.1007/s13361-018-2069-9
Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3
A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles 10.1371/journal.pone.0207051
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18
Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737
Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns 10.1039/c7cc08411k
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089
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
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381
Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054
High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols 10.1021/acsjnatprod.6b00722
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung 10.1016/j.chom.2017.10.001
Application of MALDI Mass Spectrometry in Natural Products Analysis 10.1055/s-0042-104800
From Sample to Multi-Omics Conclusions in under 48 Hours 10.1128/mSystems.00038-16
Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113
A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry 10.1016/j.aca.2015.01.002
Illuminating the dark matter in metabolomics 10.1073/pnas.1516878112
Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing 10.1039/c3np70086k
ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics 10.1093/bioinformatics/btu019
Queen signals in a stingless bee: suppression of worker ovary activation and spatial distribution of active compounds 10.1038/srep07449
Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis 10.1128/MSYSTEMS.00375-19
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/J.FOODCHEM.2019.125290
In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation 10.1016/J.FOODCHEM.2019.05.099
Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation 10.1021/ACS.JNATPROD.8B00916
The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/S12915-019-0660-6
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L 10.3389/FPLS.2019.00846
Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin 10.1021/ACS.ANALCHEM.8B05854
Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9
Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim 10.1021/acsinfecdis.9b00513
Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9
Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292
Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6
Time-Scale Shifting of Volatile Semiochemical Levels in Wild Type Lychnophora ericoides (Brazilian arnica) and Pollinator Records 10.1055/a-1320-4556
Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells 10.1038/s41419-020-03275-2
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020
Convergent evolution of pain-inducing defensive venom components in spitting cobras 10.1126/science.abb9303
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/msystems.00601-21
REDES MOLECULARES: UMA ANÁLISE SOBRE ANOTAÇÕES E DESCOBERTA DE NOVOS ATIVOS 10.21577/0100-4042.20170777
CHAPTER 10. Perspectives for the Future 10.1039/9781788010399-00264
CHAPTER 3. Metabolomics 10.1039/9781788010399-00057
Mass Spectrometry in Chemical Biology 10.1039/9781788010399
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
Anupriya Tripathi
Tripathi Anupriya
ORCID: 0000-0001-8912-9684
Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063
Links between gut microbiome composition and fatty liver disease in a large population sample 10.1101/2020.07.30.20164962
The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361
Links between gut microbiome composition and fatty liver disease in a large population sample 10.1080/19490976.2021.1888673
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21
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
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