ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics
Silva, Ricardo R. Jourdan, Fabien Salvanha, Diego M. Letisse, Fabien Jamin, Emilien L. Guidetti-Gonzalez, Simone Labate, Carlos A. Vencio, Ricardo Z. N.
Létisse Fabien
Fabien Létisse
ORCID: 0000-0002-1490-0152
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Simultaneous Measurement of Metabolite Concentration and Isotope Incorporation by Mass Spectrometry 10.1021/acs.analchem.9b05709
Control and regulation of acetate overflow in Escherichia coli 10.1101/2020.08.18.255356
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Functional genomics of the muscle response to restraint and transport in chickens 10.2527/jas.2010-3288
ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics 10.1093/bioinformatics/btu019
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Crucial Role of ppGpp in the Resilience of Escherichia coli to Growth Disruption 10.1128/mSphere.01132-20
The influence of metabolic network structures and energy requirements on xanthan gum yields 10.1016/S0168-1656(02)00221-3
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Control and regulation of acetate overflow in Escherichia coli 10.7554/eLife.63661
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Combining metabolomics and gene expression analysis reveals that propionyl- and butyryl-carnitines are involved in late stages of arbuscular mycorrhizal symbiosis 10.1093/mp/sst136
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Functional Analysis of Deoxyhexose Sugar Utilization in Escherichia coli Reveals Fermentative Metabolism under Aerobic Conditions 10.1128/AEM.00719-21
Carlos Alberto Labate
Labate Carlos Alberto / C.A.Labate / C. Labate
ORCID: 0000-0001-7309-1300
Targeted Metabolic Profiles of the Leaves and Xylem Sap of Two Sugarcane Genotypes Infected with the Vascular Bacterial Pathogen Leifsonia xyli subsp. xyli 10.3390/metabo11040234
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Network Analyses and Data Integration of Proteomics and Metabolomics From Leaves of Two Contrasting Varieties of Sugarcane in Response to Drought 10.3389/fpls.2019.01524
Distinct leaf transcriptomic response of water deficient Eucalyptus grandis submitted to potassium and sodium fertilization 10.1371/journal.pone.0218528
Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa 10.3390/ijms20081975
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Sugarcane must fed-batch fermentation by Saccharomyces cerevisiae: impact of sterilized and non-sterilized sugarcane must 10.1007/s10482-019-01250-2
The Eucalyptus Cuticular Waxes Contribute in Preformed Defense Against Austropuccinia psidii 10.3389/fpls.2018.01978
Cell Wall Proteome of Sugarcane Young and Mature Leaves and Stems 10.1002/pmic.201700129
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Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production 10.1093/femsle/fnx159
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Development of a quantitative real-time PCR assay using SYBR Green for early detection and quantification of Austropuccinia psidii in Eucalyptus grandis 10.1007/s10658-017-1321-7
Proteomic profiling identifies N-acetylmuramoyl-l-alanine amidase as a novel biomarker of sepsis 10.2217/bmm-2016-0184
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Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis 10.3389/fpls.2016.00932
Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases 10.1186/s12870-015-0677-0
Label-Free Quantitative Proteomic Analysis of Puccinia psidii Uredospores Reveals Differences of Fungal Populations Infecting Eucalyptus and Guava 10.1371/journal.pone.0145343
Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size 10.1021/acs.jafc.5b04376
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Prospection and Evaluation of (Hemi) Cellulolytic Enzymes Using Untreated and Pretreated Biomasses in Two Argentinean Native Termites 10.1371/journal.pone.0136573
Evaluating the composition and processing potential of novel sources of Brazilian biomass for sustainable biorenewables production 10.1186/1754-6834-7-10
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The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella 10.1371/journal.ppat.1009326
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
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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
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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
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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
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
Fabien Jourdan
Jourdan Fabien
ORCID: 0000-0001-9401-2894
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Dynamic Metabolic Disruption in Rats Perinatally Exposed to Low Doses of Bisphenol-A. 10.1371/journal.pone.0141698
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Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. 10.1007/s11306-009-0196-9
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Metabolic network visualization eliminating node redundance and preserving metabolic pathways. 10.1186/1752-0509-1-29
Bisphenol A Exposure Disrupts Neurotransmitters Through Modulation of Transaminase Activity in the Brain of Rodents. 10.1210/en.2016-1207
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Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas 10.3390/metabo8030051
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud 10.1093/gigascience/giy149
Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation 10.1021/acs.jproteome.8b00524
An Untargeted Metabolomics Approach to Investigate the Metabolic Modulations of HepG2 Cells Exposed to Low Doses of Bisphenol A and 17β-Estradiol 10.3389/fendo.2018.00571
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Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig 10.3390/nu12082442
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Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126 10.1007/s00204-018-2235-7
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks 10.1371/journal.pcbi.1008730
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases 10.1101/2021.02.12.430944
Pathway analysis in metabolomics: pitfalls and best practice for the use of over-representation analysis 10.1101/2021.05.24.445406
Chapter Eight - Plant genome-scale metabolic networks 10.1016/bs.abr.2020.09.021
Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring 10.33594/000000377
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Milk metabolome reveals variations on enteric methane emissions from dairy cows fed a specific inhibitor of the methanogenesis pathway 10.3168/jds.2021-20477