Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
Alan K. Jarmusch Mingxun Wang Christine M. Aceves Rohit S. Advani Shaden Aguire Alexander A. Aksenov Gajender Aleti Allegra T. Aron Anelize Bauermeister Sanjana Bolleddu Amina Bouslimani Andres Mauricio Caraballo Rodriguez Rama Chaar Roxana Coras Emmanuel O. Elijah Madeleine Ernst Julia M. Gauglitz Emily C. Gentry Makhai Husband Scott A. Jarmusch Kenneth L. Jones, II Zdenek Kamenik Audrey Le Gouellec Aileen Lu Laura-Isobel McCall Kerry L. McPhail Michael J. Meehan Alexey V. Melnik Riya C. Menezes Yessica Alejandra Montoya Giraldo Ngoc Hung Nguyen Louis Felix Nothias Mélissa Nothias-Esposito Morgan Panitchpakdi Daniel Petras Robert Quinn Nicole Sikora Justin J.J. van der Hooft Fernando Vargas Alison Vrbanac Kelly Weldon Rob Knight Nuno Bandeira Pieter C. Dorrestein
bioRxiv, 2019-8-29
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
Alexander Aksenov
Aksenov Alexander
ORCID: 0000-0002-9445-2248
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information 10.1038/s41592-019-0344-8
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471
Learning representations of microbe–metabolite interactions 10.1038/s41592-019-0616-3
Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9
Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome 10.1128/mSystems.00901-19
ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7
A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles 10.1126/scitranslmed.aay5445
Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0
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
audrey Le Gouellec
Le Gouellec audrey
ORCID: 0000-0002-4905-3854
High-Resolution Magic Angle Spinning NMR-Based Metabolomics Revealing Metabolic Changes in Lung of Mice Infected with P. aeruginosa Consistent with the Degree of Disease Severity 10.1021/acs.jproteome.8b00306
A PBP2x from a Clinical Isolate ofStreptococcus pneumoniaeExhibits an Alternative Mechanism for Reduction of Susceptibility to β-Lactam Antibiotics 10.1074/jbc.m313492200
In vitro reconstitution of a trimeric complex of DivIB, DivIC and FtsL, and their transient co-localization at the division site in Streptococcus pneumoniae 10.1111/j.1365-2958.2004.04408.x
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae. 10.1074/jbc.M408446200
Central domain of DivIB caps the C-terminal regions of the FtsL/DivIC coiled-coil rod. 10.1074/jbc.M109.019471
Optimization of Antitumor Immunotherapy Mediated by Type III Secretion System-based Live Attenuated Bacterial Vectors 10.1097/CJI.0b013e31824747e5
A safe bacterial microsyringe for in vivo antigen delivery and immunotherapy 10.1038/mt.2013.41
Scavenging of reactive oxygen species by tryptophan metabolites helps Pseudomonas aeruginosa escape neutrophil killing 10.1016/j.freeradbiomed.2014.06.003
Is tryptophan metabolism involved in sleep apnea-related cardiovascular co-morbidities and cancer progression? 10.1016/j.mehy.2015.06.022
Roles of pneumococcal DivIB in cell division. 10.1128/JB.00376-08
Bacterial vectors for active immunotherapy reach clinical and industrial stages 10.4161/hv.21429
Live-attenuated bacteria as a cancer vaccine vector 10.1586/14760584.2013.836914
Bacterial vectors for the delivery of tumor antigens 10.1007/978-1-4939-0345-0_33
Poly-functional and long-lasting anticancer immune response elicited by a safe attenuated Pseudomonas aeruginosa vector for antigens delivery 10.1038/mto.2016.33
Targeted release of transcription factors for cell reprogramming by a natural micro-syringe 10.1016/j.ijpharm.2016.09.081
Cibler les mécanismes immunosuppresseurs de la réponse immune antitumorale en onco-hématologie : une nouvelle stratégie thérapeutique ? Immune checkpoint blockade in onco-hematology therapy. 10.1684/ito.2017.0078
Chemobacterial Synthesis of a Sialyl-Tn Cyclopeptide Vaccine Candidate 10.1002/cbic.201700240
Altered humoral immune responses and IgG subtypes in NOX2-deficient mice and patients: A key role for NOX2 in antigen-presenting cells 10.3389/fimmu.2018.01555
Tryptophan catabolism in Pseudomonas aeruginosa and potential for inter-kingdom relationship 10.1186/s12866-016-0756-x
Killed but metabolically active Pseudomonas aeruginosa-based vaccine induces protective humoral- and cell-mediated immunity against Pseudomonas aeruginosa pulmonary infections 10.1016/j.vaccine.2018.02.040
Effect of double-filtration plasmapheresis for antibody-mediated rejection on hemostasis parameters and thrombin generation 10.1016/j.thromres.2018.04.018
Corrigendum to “Effect of double-filtration plasmapheresis for antibody-mediated rejection on hemostasis parameters and thrombin generation” [Thromb. Res. 166 (2018) 113–121](S0049384818303232)(10.1016/j.thromres.2018.04.018) 10.1016/j.thromres.2018.05.033
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471
ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7
Ion Identity Molecular Networking in the GNPS Environment 10.1101/2020.05.11.088948
Prebiotic role of softwood hemicellulose in healthy mice model 10.1016/j.jff.2019.103688
Mediation analysis of CRP on the association of physical activity with FEV1 and FVC: the ECRHS study. 10.1183/13993003.congress-2018.pa4483
Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6
COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella 10.3389/fimmu.2020.01714
The role of C-reactive protein levels on the association of physical activity with lung function in adults 10.1371/journal.pone.0222578
Optimal epitope composition after antigen screening using a live bacterial delivery vector application to TRP-2 10.4161/bbug.1.1.9482
Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections 10.3390/metabo11020063
What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk 10.3390/metabo11060406
Christine Aceves
Aceves Christine
ORCID: 0000-0002-2543-8936
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471
Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159