Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
Mehdi A. Beniddir
Kyo Bin Kang
Grégory Genta-Jouve
Florian Huber
Simon Rogers
Justin J. J. van der Hooft
Natural Product Reports, 2021
Grégory Genta-Jouve
Genta-Jouve Grégory
ORCID: 0000-0002-9239-4371
Hygroline derivatives from Schizanthus tricolor and their anti-trypanosomatid and antiplasmodial activities
10.1016/j.phytochem.2021.112957
Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification
10.1016/j.cbpa.2016.12.022
Ecdysonelactones, Ecdysteroids from the Tropical Eastern Pacific Zoantharian Antipathozoanthus hickmani
10.3390/md16020058
Griseofamines A and B: Two Indole-Tetramic Acid Alkaloids with 6/5/6/5 and 6/5/7/5 Ring Systems from Penicillium griseofulvum
10.1021/acs.orglett.8b00584
Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification
http://dx.doi.org/10.1016/j.cbpa.2016.12.022
Allelopathic interactions between the brown algal genus Lobophora (Dictyotales, Phaeophyceae) and scleractinian corals
10.1038/srep18637
Antimicrobial Oligophenalenone Dimers from the Soil Fungus Talaromyces stipitatus
10.1021/acs.jnatprod.6b00458
Gersemiols A-C and Eunicellol A, Diterpenoids from the Arctic Soft Coral Gersemia fruticosa
10.1021/acs.jnatprod.6b00040
Talaroketals A and B, unusual bis(oxaphenalenone) spiro and fused ketals from the soil fungus Talaromyces stipitatus ATCC 10500
10.1039/c5ob02657a
Three new trixane glycosides obtained from the leaves of Jungia sellowii Less. using centrifugal partition chromatography
10.3762/bjoc.12.68
Chiroptical study and absolute configuration of securinine oxidation products
10.1080/14786419.2015.1023727
Cymoside, a monoterpene indole alkaloid with a hexacyclic fused skeleton from Chimarrhis cymosa
10.1016/j.tetlet.2015.07.066
Cystophloroketals A-E, Unusual Phloroglucinol-Meroterpenoid Hybrids from the Brown Alga Cystoseira tamariscifolia
10.1021/acs.jnatprod.5b00264
Eryloside W, a triterpenoid saponin from the sponge Dictyonella marsilii
10.1016/j.phytol.2015.07.004
Gambierone, a Ladder-Shaped Polyether from the Dinoflagellate Gambierdiscus belizeanus
10.1021/acs.orglett.5b00902
Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae
10.1038/srep08282
MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis
10.1093/bioinformatics/btu740
Unexpected talaroenamine derivatives and an undescribed polyester from the fungus Talaromyces stipitatus ATCC10500
10.1016/j.phytochem.2015.09.002
Autumnalamide, a Prenylated Cyclic Peptide from the Cyanobacterium Phormidium autumnale, Acts on SH-SY5Y Cells at the Mitochondrial Level
10.1021/np500374a
Comparative LC-MS-based metabolite profiling of the ancient tropical rainforest tree Symphonia globulifera
10.1016/j.phytochem.2014.09.009
Development of a Work-Flow for High-Performance Thin-Layer Chromatography Data Processing for Untargeted Metabolomics
10.1556/jpc.27.2014.5.1
Environmental solutions for the sustainable production of bioactive natural products from the marine sponge Crambe crambe
10.1016/j.scitotenv.2013.12.068
Mahorones, Highly Brominated Cyclopentenones from the Red Alga Asparagopsis taxiformis
10.1021/np401094h
Rapid Identification of Antioxidant Compounds of Genista saharae Coss. & Dur. by Combination of DPPH Scavenging Assay and HPTLC-MS
10.3390/molecules19044369
Two-dimensional ultra high pressure liquid chromatography quadrupole/time-of-flight mass spectrometry for semi-targeted natural compounds identification
10.1016/j.phytol.2014.10.029
Biosynthesis in marine sponges: the radiolabelling strikes back
10.1007/s11101-012-9225-9
Packaging and Delivery of Chemical Weapons: A Defensive Trojan Horse Stratagem in Chromodorid Nudibranchs
10.1371/journal.pone.0062075
Revising the Absolute Configurations of Coatlines via Density Functional Theory Calculations of Electronic Circular Dichroism Spectra
10.1002/chir.22129
Additional bioactive guanidine alkaloids from the Mediterranean sponge Crambe crambe
10.1039/c2ra00045h
Comparative bioaccumulation kinetics of trace elements in Mediterranean marine sponges
10.1016/j.chemosphere.2012.04.052
Determination of the absolute configuration and evaluation of the in vitro antitumor activity of dilospirane B
10.1016/j.phytol.2012.08.005
SPONGE CHEMICAL DIVERSITY: FROM BIOSYNTHETIC PATHWAYS TO ECOLOGICAL ROLES
10.1016/b978-0-12-394283-8.00004-7
Acanthifoliosides, minor steroidal saponins from the Caribbean sponge Pandaros acanthifolium
10.1016/j.tet.2010.11.103
New Insight into Marine Alkaloid Metabolic Pathways: Revisiting Oroidin Biosynthesis
10.1002/cbic.201100449
Structure elucidation of the new citharoxazole from the Mediterranean deep-sea sponge Latrunculia (Biannulata) citharistae
10.1002/mrc.2772
Njaoaminiums A, B, and C: Cyclic 3-Alkylpyridinium Salts from the Marine Sponge Reniera sp
10.3390/molecules14114716
Parazoanthines A-E, Hydantoin Alkaloids from the Mediterranean Sea Anemone Parazoanthus axinellae
10.1021/np900437y
Steroidal glycosides from the marine sponge Pandaros acanthifolium
10.1016/j.steroids.2009.03.009
Terrazoanthines, 2-Aminoimidazole Alkaloids from the Tropical Eastern Pacific Zoantharian Terrazoanthus onoi
10.1021/acs.orglett.7b00369
Palladium Nanoparticle-Catalyzed Stereoretentive Cross-Coupling of Alkenyl Sulfides with Grignard Reagents
10.1021/acs.orglett.8b00208
A Reactive Eremophilane and Its Antibacterial 2(1H)-Naphthalenone Rearrangement Product, Witnesses of a Microbial Chemical Warfare
10.1021/acs.orglett.7b01788
Synthesis of a Tiacumicin B Protected Aglycone
10.1021/acs.orglett.7b01744
Absolute configuration of the new 3-epi-cladocroic acid from the mediterranean sponge Haliclona fulva
10.3390/metabo3010024
Targeted Isolation of Monoterpene Indole Alkaloids from Palicourea sessilis
10.1021/acs.jnatprod.7b00681
Polyketide Assembly Mimics and Biomimetic Access to Aromatic Rings
10.1002/9783527634606.ch13
Pleiokomenines A and B: Dimeric Aspidofractinine Alkaloids Tethered with a Methylene Group
10.1021/acs.orglett.7b03098
Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks
10.1021/acschembio.7b00413
A Nitrile Glucoside and Biflavones from the Leaves of Campylospermum excavatum (Ochnaceae)
10.1002/cbdv.201700241
Study of the Construction of the Tiacumicin B Aglycone
10.1021/acs.joc.7b02909
Antiplasmodial Securinega alkaloids from Phyllanthus fraternus: Discovery of natural (+)-allonorsecurinine
10.1016/j.tetlet.2017.08.045
Introducing the 2016 CASMI contest
10.1016/j.phytol.2017.08.007
Stereochemical Study of Puna’auic Acid, an Allenic Fatty Acid from the Eastern Indo-Pacific Cyanobacterium Pseudanabaena sp
10.1021/acs.orglett.8b00654
A Ring-Distortion Strategy from Marine Natural Product Ilimaquinone Leads to Quorum Sensing Modulators
10.1002/ejoc.201800047
MS/MS-Guided Isolation of Clarinoside, a New Anti-Inflammatory Pentalogin Derivative
10.3390/molecules23051237
Mucorolactone, a Macrolactone from Mucor sp. SNB-VECD13A, a Fungus Isolated from the Cuticle of a Vespidae Species
10.1021/acs.orglett.8b01367
Tsavoenones A–C: unprecedented polyketides with a 1,7-dioxadispiro[4.0.4.4]tetradecane core from the lichen Parmotrema tsavoense
10.1039/C8OB01280F
Anti-inflammatory and antiproliferative diterpenoids from Plectranthus scutellarioides
10.1016/j.phytochem.2018.06.012
Resolving the (19R) Absolute Configuration of Lanciferine, a Monoterpene Indole Alkaloid from Alstonia boulindaensis
10.1021/acs.jnatprod.7b00957
Sanctis A-C: Three racemic procyanidin analogues from the lichen Parmotrema sancti-angelii
10.1002/ejoc.201800202
The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research
10.1039/c7np00064b
Metabolome consistency: additional parazoanthines from the Mediterranean zoanthid Parazoanthus axinellae
10.3390/metabo4020421
Callyspongidic Acids: Amphiphilic Diacids from the Tropical Eastern Pacific Sponge Callyspongia cf. californica
10.1021/acs.jnatprod.8b00683
MS/MS-Guided Isolation of Clarinoside, a New Anti-Inflammatory Pentalogin Derivative
10.20944/preprints201803.0209.v1
MS/MS-Guided Isolation of Clarinoside, a New Anti-Inflammatory Pentalogin Derivative
10.20944/preprints201803.0209.v2
Insights into the Biosynthesis of Cyclic Guanidine Alkaloids from Crambeidae Marine Sponges
10.1002/anie.201809539
Insights into the Biosynthesis of Cyclic Guanidine Alkaloids from Crambeidae Marine Sponges
10.1002/ange.201809539
Treasures from the Deep: Characellides as Anti-Inflammatory Lipoglycotripeptides from the Sponge Characella pachastrelloides
10.1021/acs.orglett.8b03684
Biosynthetic investigation of γ-lactones in Sextonia rubra wood using in situ TOF-SIMS MS/MS imaging to localize and characterize biosynthetic intermediates
10.1038/s41598-018-37577-5
Structure Revision of Microginins 674 and 690 from the Cultured Cyanobacterium Microcystis aeruginosa
10.1021/acs.jnatprod.9b00015
Stereoselective Access to (E)-1,3-Enynes through Pd/Cu-Catalyzed Alkyne Hydrocarbation of Allenes
10.1021/acs.orglett.9b00828
Halogenated Tyrosine Derivatives from the Tropical Eastern Pacific Zoantharians Antipathozoanthus hickmani and Parazoanthus darwini
10.1021/acs.jnatprod.9b00173
Bromotryptamine and Bromotyramine Derivatives from the Tropical Southwestern Pacific Sponge Narrabeena nigra
10.3390/md17060319
CANPA: Computer-Assisted Natural Products Anticipation
10.1021/acs.analchem.9b02216
Bioactive Diketopiperazines and Nucleoside Derivatives from a Sponge-Derived Streptomyces Species
10.3390/md17100584
Marine natural products from zoantharians: bioactivity, biosynthesis, systematics, and ecological roles
10.1039/C9NP00043G
Cytotoxic and Anti-Inflammatory Effects of Ent-Kaurane Derivatives Isolated from the Alpine Plant Sideritis hyssopifolia
10.3390/molecules25030589
Total Synthesis of Tiacumicin B: Implementing Hydrogen Bond Directed Acceptor Delivery for Highly Selective β‐Glycosylations
10.1002/anie.202000231
Total Synthesis of Tiacumicin B: Implementing Hydrogen Bond Directed Acceptor Delivery for Highly Selective β‐Glycosylations
10.1002/ange.202000231
Lipid Annotation by Combination of UHPLC-HRMS (MS), Molecular Networking, and Retention Time Prediction: Application to a Lipidomic Study of In Vitro Models of Dry Eye Disease
10.3390/metabo10060225
Futunamine, a Pyrrole–Imidazole Alkaloid from the Sponge Stylissa aff. carteri Collected off the Futuna Islands
10.1021/acs.jnatprod.0c00223
Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus
10.1021/acs.joc.0c01210
Magnificines A and B, Antimicrobial Marine Alkaloids Featuring a Tetrahydrooxazolo[3,2-a]azepine-2,5(3H,6H)-dione Backbone from the Red Sea Sponge Negombata magnifica
10.3390/md19040214
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
10.1039/D1NP00023C
Untargeted Metabolomics Approach for the Discovery of Environment-Related Pyran-2-Ones Chemodiversity in a Marine-Sourced Penicillium restrictum
10.3390/md19070378
Fusaripyridines A and B; Highly Oxygenated Antimicrobial Alkaloid Dimers Featuring an Unprecedented 1,4-Bis(2-hydroxy-1,2-dihydropyridin-2-yl)butane-2,3-dione Core from the Marine Fungus Fusarium sp. LY019
10.3390/md19090505
Identification of Antagonistic Compounds between the Palm Tree Xylariale Endophytic Fungi and the Phytopathogen Fusarium oxysporum
10.1021/acs.jafc.1c03141
Florian Huber
Huber Florian
ORCID: 0000-0002-3535-9406
Cytoskeletal crosstalk: When three different personalities team up
10.1016/j.ceb.2014.10.005
Robust organizational principles of protrusive biopolymer networks in migrating living cell
10.1371/journal.pone.0014471
Self-regulative organization of the cytoskeleton
10.1002/cm.20509
Emergent complexity of the cytoskeleton: From single filaments to tissue
10.1080/00018732.2013.771509
Counterion-induced formation of regular actin bundle networks
10.1039/c1sm06019h
Actin-microtubule coordination at growing microtubule ends
10.1038/ncomms5778
In vitro reconstitution of dynamic microtubules interacting with actin filament networks
10.1016/B978-0-12-397924-7.00017-0
Growing actin networks form lamellipodium and lamellum by self-assembly
10.1529/biophysj.108.134817
Formation of regularly spaced networks as a general feature of actin bundle condensation by entropic forces
10.1088/1367-2630/17/4/043029
Actin droplet machine
10.1098/rsos.191135
GGIR: A Research Community–Driven Open Source R Package for Generating Physical Activity and Sleep Outcomes From Multi-Day Raw Accelerometer Data
10.1123/jmpb.2018-0063
Computing on actin bundles network
10.1038/s41598-019-51354-y
Actin networks voltage circuits
10.1103/PhysRevE.101.052314
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
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
10.1101/2021.04.18.440324
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
10.1039/D1NP00023C
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
