Feature-based molecular networking in the GNPS analysis environment
Louis-Félix Nothias Daniel Petras Robin Schmid Kai Dührkop Johannes Rainer Abinesh Sarvepalli Ivan Protsyuk Madeleine Ernst Hiroshi Tsugawa Markus Fleischauer Fabian Aicheler Alexander A. Aksenov Oliver Alka Pierre-Marie Allard Aiko Barsch Xavier Cachet Andres Mauricio Caraballo-Rodriguez Ricardo R. Da Silva Tam Dang Neha Garg Julia M. Gauglitz Alexey Gurevich Giorgis Isaac Alan K. Jarmusch Zdeněk Kameník Kyo Bin Kang Nikolas Kessler Irina Koester Ansgar Korf Audrey Le Gouellec Marcus Ludwig Christian Martin H. Laura-Isobel McCall Jonathan McSayles Sven W. Meyer Hosein Mohimani Mustafa Morsy Oriane Moyne Steffen Neumann Heiko Neuweger Ngoc Hung Nguyen Melissa Nothias-Esposito Julien Paolini Vanessa V. Phelan Tomáš Pluskal Robert A. Quinn Simon Rogers Bindesh Shrestha Anupriya Tripathi Justin J. J. van der Hooft Fernando Vargas Kelly C. Weldon Michael Witting Heejung Yang Zheng Zhang Florian Zubeil Oliver Kohlbacher Sebastian Böcker Theodore Alexandrov Nuno Bandeira Mingxun Wang Pieter C. Dorrestein
Nature Methods, 2020-8-24
Kyo Bin Kang
Kang Kyo Bin
ORCID: 0000-0003-3290-1017
Email: kbkang@sookmyung.ac.kr
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Identification of glucocorticoid-response genes in children with acute lymphoblastic leukemia 10.1182/blood-2005-07-2853
Glucocorticoid-induced apoptosis and glucocorticoid resistance in acute lymphoblastic leukemia 10.1016/j.jsbmb.2004.12.017
Glucocorticoid-induced apoptosis and glucocorticoid resistance: molecular mechanisms and clinical relevance 10.1038/sj.cdd.4401456
Client-Server environment for high-performance gene expression data analysis 10.1093/bioinformatics/btg074
The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells 10.1186/s12864-018-4876-6
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees 10.1093/bioinformatics/bty541
ensembldb: an R package to create and use Ensembl-based annotation resources 10.1093/bioinformatics/btz031
Influence of collection tubes during quantitative targeted metabolomics studies in human blood samples 10.1016/j.cca.2018.08.014
The metaRbolomics Toolbox in Bioconductor and beyond 10.3390/metabo9100200
Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404
MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data 10.1101/2020.04.29.067868
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MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data 10.1021/acs.jproteome.0c00313
Metabolic Signature of Arrhythmogenic Cardiomyopathy 10.3390/metabo11040195
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment 10.1038/s41467-021-23953-9
Pierre-Marie Allard
Allard Pierre-Marie
ORCID: 0000-0003-3389-2191
Email: pierre-marie.allard@unige.ch
Thinking big about small beings--the (yet) underdeveloped microbial natural products chemistry in Brazil. 10.1039/c3np70112c
Antiviral chlorinated daphnane diterpenoid orthoesters from the bark and wood of Trigonostemon cherrieri. 10.1016/j.phytochem.2012.07.023
Trigocherrin A, the first natural chlorinated daphnane diterpene orthoester from Trigonostemon cherrieri. 10.1021/ol2030907
Alkylated flavanones from the bark of Cryptocarya chartacea as dengue virus NS5 polymerase inhibitors. 10.1021/np200715v
Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification 10.1016/j.cbpa.2016.12.022
Pharmacognosy in the digital era: shifting to contextualized metabolomics 10.1016/j.copbio.2018.02.010
Lung Cancer Chemopreventive Activity of Patulin Isolated from Penicillium vulpinum 10.3390/molecules23030636
Searching for original natural products by molecular networking: detection, isolation and total synthesis of chloroaustralasines 10.1039/C8QO00429C
The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis 10.7554/eLife.37082
Application of a molecular networking approach for clinical and forensic toxicology exemplified in three cases involving 3‐MeO‐PCP, doxylamine, and chlormequat 10.1002/dta.2550
Characterization, Diversity, and Structure-Activity Relationship Study of Lipoamino Acids from Pantoea sp. and Synthetic Analogues 10.3390/ijms20051083
Taxonomically informed scoring enhances confidence in natural products annotation 10.1101/702308
Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism 10.3390/molecules25122954
In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease 10.26434/chemrxiv.13065206
In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease 10.26434/chemrxiv.13065206.v1
Spatial and evolutionary predictability of phytochemical diversity 10.1073/pnas.2013344118
Novel trophic interactions under climate change promote alpine plant coexistence 10.1126/science.abd7015
Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata 10.1101/2021.02.28.433265
A Mass Spectrometry Based Metabolite Profiling Workflow for Selecting Abundant Specific Markers and Their Structurally Related Multi-Component Signatures in Traditional Chinese Medicine Multi-Herb Formulae. 10.3389/fphar.2020.578346
New insights into quetiapine metabolism using molecular networking. 10.1038/s41598-020-77106-x
Feature-based molecular networking in the GNPS analysis environment. 10.1038/s41592-020-0933-6
Insights on the Structural and Metabolic Resistance of Potato (Solanum tuberosum) Cultivars to Tuber Black Dot (Colletotrichum coccodes). 10.3389/fpls.2020.01287
Metabolite Profiling of Javanese Ginger Zingiber purpureum and Identification of Antiseizure Metabolites via a Low-Cost Open-Source Zebrafish Bioassay-Guided Isolation. 10.1021/acs.jafc.0c02641
Surface sensing triggers a broad-spectrum antimicrobial response in Pseudomonas aeruginosa. 10.1111/1462-2920.15139
A database of high-resolution MS/MS spectra for lichen metabolites. 10.1038/s41597-019-0305-1
Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation. 10.3389/fpls.2019.01329
Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404
Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time. 10.3389/fmicb.2019.02042
Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking. 10.3390/molecules24162989
Identification of chemotypes in bitter melon by metabolomics: a plant with potential benefit for management of diabetes in traditional Chinese medicine. 10.1007/s11306-019-1565-7
A case of fatal acebutolol poisoning: an illustration of the potential of molecular networking. 10.1007/s00414-019-02062-9
Targeted Isolation of Monoterpene Indole Alkaloids from Palicourea sessilis. 10.1021/acs.jnatprod.7b00681
Cytotoxic Prenylated Stilbenes Isolated from Macaranga tanarius. 10.1021/acs.jnatprod.7b00409
Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks. 10.1021/acschembio.7b00413
Peptidomic and transcriptomic profiling of four distinct spider venoms. 10.1371/journal.pone.0172966
UHPLC-MS-based HDAC Assay Applied to Bio-guided Microfractionation of Fungal Extracts. 10.1002/pca.2652
Targeted Isolation of Indolopyridoquinazoline Alkaloids from Conchocarpus fontanesianus Based on Molecular Networks. 10.1021/acs.jnatprod.6b00379
Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells 10.3390/ijms22126467
Drug Repurposing to Identify a Synergistic High-Order Drug Combination to Treat Sunitinib-Resistant Renal Cell Carcinoma 10.3390/cancers13163978
Vanessa Phelan
Phelan Vanessa / Vanessa V Phelan / Vanessa Phelan
ORCID: 0000-0001-7156-9294
Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa 10.1128/JB.01258-13
Lipophilic mediated assays for ß-hematin inhibitors 10.2174/138620710790980496
MS/MS networking guided analysis of molecule and gene cluster families 10.1073/pnas.1303471110
Phosphonopeptide K-26 biosynthetic intermediates in Astrosporangium hypotensionis 10.1039/b611768f
Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome 10.1038/ismej.2015.207
Interkingdom metabolic transformations captured by microbial imaging mass spectrometry 10.1073/pnas.1206855109
Benzodiazepine Biosynthesis in Streptomyces refuineus 10.1016/j.chembiol.2007.05.009
Reassembly of anthramycin biosynthetic gene cluster by using recombinogenic cassettes 10.1002/cbic.200800029
Adenylation Enzyme Characterization Using γ -18O4-ATP Pyrophosphate Exchange 10.1016/j.chembiol.2009.04.007
Primer on Agar-Based Microbial Imaging Mass Spectrometry 10.1128/JB.00823-12
Benzodiazepine Biosynthesis in Streptomyces refuineus (DOI:10.1016/j.chembiol.2007.05.009) 10.1016/j.chembiol.2007.07.006
Mass spectrometry analysis of pseudomonas aeruginosa treated with azithromycin 10.1007/s13361-015-1101-6
Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle 10.1074/jbc.M110.201350
Microbial metabolic exchangeg-the chemotype-to-phenotype link 10.1038/nchembio.739
Microbial metabolic exchange in 3D 10.1038/ismej.2012.155
Microbiome and metabolome data integration provides insight into health and disease 10.1016/j.trsl.2017.07.001
Natural products as mediators of disease 10.1039/c6np00063k
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9
Feature-Based Molecular Networking for Metabolite Annotation. 10.1007/978-1-0716-0239-3_13
Exogenous Alginate Protects Staphylococcus aureus from Killing by Pseudomonas aeruginosa. 10.1128/jb.00559-19
Feature-based molecular networking in the GNPS analysis environment. 10.1038/s41592-020-0933-6
Artificial Sputum Medium Formulation Impacts Pseudomonas aeruginosa Phenotype and Chemotype 10.1101/2021.01.25.428197
Michael Witting
Witting Michael
ORCID: 0000-0002-1462-4426
Email: michael.witting@helmholtz-muenchen.de
Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past 10.1073/pnas.1500783112
Fast separation and quantification of steroid hormones δ4- and δ7-dafachronic acid in Caenorhabditis elegans 10.1016/j.jchromb.2014.12.005
DI-ICR-FT-MS-based high-throughput deep metabotyping: a case study of the Caenorhabditis elegans-Pseudomonas aeruginosa infection model 10.1007/s00216-014-8331-5
Optimizing a ultrahigh pressure liquid chromatography-time of flight-mass spectrometry approach using a novel sub-2μm core-shell particle for in depth lipidomic profiling of Caenorhabditis elegans 10.1016/j.chroma.2014.07.021
Integrating analytical resolutions in non-targeted wine metabolomics 10.1016/j.tet.2015.02.054
Ultrahigh resolution mass spectrometry based non-targeted microbial metabolomics 10.1007/978-1-4614-1689-0_5
Molecular and structural characterization of dissolved organic matter during and post cyanobacterial bloom in Taihu by combination of NMR spectroscopy and FTICR mass spectrometry 10.1016/j.watres.2014.02.051
Transcriptome and Metabolome Data Integration-Technical Perquisites for Successful Data Fusion and Visualization 10.1016/B978-0-444-62651-6.00018-0
Ultrahigh resolution mass spectrometry-based metabolic characterization reveals cerebellum as a disturbed region in two animal models 10.1016/j.talanta.2013.09.019
Steroid hormone signalling links reproduction to lifespan in dietary-restricted Caenorhabditis elegans 10.1038/ncomms5879
Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia coli and Shigella, completely overlapping in antisense to yaaW 10.1111/1574-6968.12288
Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet 10.1038/ismej.2014.79
High-resolution metabolite imaging of light and dark treated retina using MALDI-FTICR mass spectrometry 10.1002/pmic.201300407
Masstrix reloaded: Combined analysis and visualization of tran-scriptome and metabolome data 10.1371/journal.pone.0039860
Metformin impacts cecal bile acid profiles in mice 10.1016/j.jchromb.2018.02.029
Pharmacometabolic response to pirfenidone in pulmonary fibrosis detected by MALDI-FTICR-MSI 10.1183/13993003.02314-2017
Metabotype variation in a field population of tansy plants influences aphid host selection 10.1111/pce.13407
Tandem HILIC-RP liquid chromatography for increased polarity coverage in food analysis 10.1002/elps.201800038
Usage of FT-ICR-MS Metabolomics for Characterizing the Chemical Signatures of Barrel-Aged Whisky. 10.3389/fchem.2018.00029
Mycorrhiza-triggered transcriptomic and metabolomic networks impinge on herbivore fitness 10.1104/pp.17.01810
Bio- and chemoinformatics approaches for metabolomics data analysis 10.1007/978-1-4939-7643-0_4
Identification of molecules from non-targeted analysis 10.1016/j.jchromb.2017.11.030
WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series. 10.1080/21624054.2017.1373939
Comparative analysis of LytS/LytTR-type histidine kinase/response regulator systems in γ-proteobacteria 10.1371/journal.pone.0182993
Identification of a High-Affinity Pyruvate Receptor in Escherichia coli 10.1038/s41598-017-01410-2
LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome 10.1371/journal.pone.0172311
QSRR modeling for metabolite standards analyzed by two different chromatographic columns using multiple linear regression 10.3390/metabo7010007
Amniotic Fluid and Maternal Serum Metabolic Signatures in the Second Trimester Associated with Preterm Delivery 10.1021/acs.jproteome.6b00845
Metabolic profile of human coelomic fluid 10.4155/bio-2016-0223
The role of dafachronic acid signaling in development and longevity in Caenorhabditis elegans: Digging deeper using cutting-edge analytical chemistry 10.3389/fendo.2016.00012
Natural oxygenation of Champagne wine during ageing on lees: A metabolomics picture of hormesis 10.1016/j.foodchem.2016.02.043
Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. 10.1186/s12862-015-0558-z
Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography-tandem mass spectrometry targeted metabolomics 10.1016/j.chroma.2015.06.008
The Caenorhabditis elegans lipidome: A primer for lipid analysis in Caenorhabditis elegans 10.1016/j.abb.2015.06.003
High precision mass measurements for wine metabolomics 10.3389/fchem.2014.00102
Modeling meets metabolomics-the wormjam consensus model as basis for metabolic studies in the model organism Caenorhabditis elegans 10.3389/fmolb.2018.00096
Combined nontargeted analytical methodologies for the characterization of the chemical evolution of bottled wines 10.1021/bk-2015-1203.ch002
The sphingolipidome of the model organism Caenorhabditis elegans 10.1016/j.chemphyslip.2019.04.009
Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling 10.1016/j.jchromb.2019.01.016
In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer 10.1101/670398
The metaRbolomics Toolbox in Bioconductor and beyond 10.3390/metabo9100200
Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404
Current status of retention time prediction in metabolite identification 10.1002/jssc.202000060
Autophagy compensates for defects in mitochondrial dynamics 10.1371/journal.pgen.1008638
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model 10.3390/metabo10040130
Comprehensive vitamer profiling of folate monoand polyglutamates in baker’s yeast (Saccharomyces cerevisiae) as a function of different sample preparation procedures 10.3390/metabo10080301
Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea 10.1111/nph.16812
Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data 10.1007/978-1-0716-0239-3_18
Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6
iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine Axis 10.1016/j.celrep.2020.02.020
Reduced peroxisomal import triggers peroxisomal retrograde signaling 10.1016/j.celrep.2020.108653
UHPLC-IM-Q-ToFMS analysis of maradolipids, found exclusively in Caenorhabditis elegans dauer larvae 10.1007/s00216-021-03172-3
HLH‐30‐dependent rewiring of metabolism during starvation in C . elegans 10.1111/acel.13342
Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode 10.3390/metabo11050284
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
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BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters 10.1101/2020.08.17.240838
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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
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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
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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
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Dührkop Kai
ORCID: 0000-0002-9056-0540
Significance estimation for large scale metabolomics annotations by spectral matching 10.1038/s41467-017-01318-5
Searching molecular structure databases with tandem mass spectra using CSI:FingerID 10.1073/pnas.1509788112
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Christian Martin H.
Martin H. Christian
ORCID: 0000-0002-9604-6737
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
Fungus-Growing Ant's Microbial Interaction of Streptomyces sp. and Escovopsis sp. through Molecular Networking and MALDI Imaging 10.1177/1934578x1901400117
Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama 10.3390/md18090456
Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae) 10.3390/metabo10100406
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Koester Irina
ORCID: 0000-0002-1571-882X
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audrey Le Gouellec
Le Gouellec audrey
ORCID: 0000-0002-4905-3854
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Tam Dang
Dang Tam
ORCID: 0000-0002-3602-1917
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Total Synthesis and Biological Assessment of Novel Albicidins Discovered by Mass Spectrometric Networking 10.1002/chem.201704074
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Xavier Cachet
Cachet Xavier
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Toxic hepatitis induced by a herbal medicine: Tinospora crispa 10.1016/j.phymed.2014.04.031
Hiroshi Tsugawa
Tsugawa Hiroshi
ORCID: 0000-0002-2015-3958
The importance of bioinformatics for connecting data-driven lipidomics and biological insights 10.1016/j.bbalip.2017.05.006
Integrated Strategy for Unknown EI–MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI–MS Spectral Database, and Retention Index Prediction 10.1021/acs.analchem.7b01010
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Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics 10.3390/metabo9060119
Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404
Characterization of Lipid Profiles after Dietary Intake of Polyunsaturated Fatty Acids Using Integrated Untargeted and Targeted Lipidomics 10.3390/metabo9100241
Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics 10.3390/metabo9110251
MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas 10.1101/2020.02.11.944900
Metabolomics with 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants 10.1021/acs.analchem.9b03860
Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software 10.3390/metabo10030101
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A lipidome atlas in MS-DIAL 4 10.1038/s41587-020-0531-2
Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies 10.1021/acs.analchem.0c01980
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Metabolome-Based Discrimination Analysis of Shallot Landraces and Bulb Onion Cultivars Associated with Differences in the Amino Acid and Flavonoid Profiles 10.3390/molecules25225300
Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses 10.1016/j.isci.2020.101841
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis 10.1038/s41467-020-20508-2
Food Lipidomics for 155 Agricultural Plant Products 10.1021/acs.jafc.0c07356
OS-PCA: Orthogonal Smoothed Principal Component Analysis Applied to Metabolome Data 10.3390/metabo11030149
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Metabolomics and complementary techniques to investigate the plant phytochemical cosmos 10.1039/D1NP00014D