Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
Grímur Hjörleifsson Eldjárn
Andrew Ramsay
Justin J. J. van der Hooft
Katherine R. Duncan
Sylvia Soldatou
Juho Rousu
Rónán Daly
Joe Wandy
Simon Rogers
Sylvia Soldatou
Soldatou Sylvia
ORCID: 0000-0002-3868-102X
Email: sylvia.soldatou@gmail.com
Cold-water marine natural products, 2006 to 2016
10.1039/c6np00127k
Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery
10.1093/femsle/fnz142
Sulfated Steroid–Amino Acid Conjugates from the Irish Marine Sponge Polymastia boletiformis
10.3390/md13041632
Accramycin A, A New Aromatic Polyketide, from the Soil Bacterium, Streptomyces sp. MA37
10.3390/molecules24183384
Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential
10.1099/mic.0.000845
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Morphological, genotypic and metabolomic signatures confirm interfamilial hybridization between the ubiquitous kelps Macrocystis (Arthrothamnaceae) and Lessonia (Lessoniaceae)
10.1038/s41598-020-65137-3
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
Screening Fungal Endophytes Derived from Under-Explored Egyptian Marine Habitats for Antimicrobial and Antioxidant Properties in Factionalised Textiles
10.3390/microorganisms8101617
Comparative Metabologenomics Analysis of Polar Actinomycetes
10.3390/md19020103
Degradation of Multiple Peptides by Microcystin-Degrader Paucibacter toxinivorans (2C20)
10.3390/toxins13040265
Antimicrobial and Antibiofilm Activities of the Fungal Metabolites Isolated from the Marine Endophytes Epicoccum nigrum M13 and Alternaria alternata 13A
10.3390/md19040232
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
New directions and challenges in engineering biologically-enhanced biochar for biological water treatment.
10.1016/j.scitotenv.2021.148977
Juho Rousu
Rousu Juho
ORCID: 0000-0002-0705-4314
Email: juho.rousu@aalto.fi
Machine Learning of Protein Interactions in Fungal Secretory Pathways
10.1371/journal.pone.0159302
Multi-view kernel completion
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Predicting Protein Producibility in Filamentous Fungi
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Principal Metabolic Flux Mode Analysis
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Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
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Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models
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Classes for the masses: Systematic classification of unknowns using fragmentation spectra
10.1101/2020.04.17.046672
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification
10.1101/2020.08.19.255653
comboFM: leveraging multi-way interactions for systematic prediction of drug combination effects
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
10.1038/s41587-020-0740-8
Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects
10.1038/s41467-020-19950-z
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
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.
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HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data
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Topic modeling for untargeted substructure exploration in metabolomics
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Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics
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Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales
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Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
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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
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EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture
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MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
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In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
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Gestational-age-dependent development of the neonatal metabolome
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Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
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Predicting host taxonomic information from viral genomes: A comparison of feature representations
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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
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Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
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Comparative Metabologenomics Analysis of Polar Actinomycetes
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Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
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Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits
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PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells
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Rapid Development of Improved Data-Dependent Acquisition Strategies
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Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
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Using topic modeling to detect cellular crosstalk in scRNA-seq
10.1101/2021.07.26.453767
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
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Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit
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Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea
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Substructure-based annotation of high-resolution multistage MSn spectral trees
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Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts
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Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake
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Spectral trees as a robust annotation tool in LC-MS based metabolomics
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Metabolite identification using automated comparison of high-resolution multistage mass spectral trees
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Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi
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A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR
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Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell
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Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation
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Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae)
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Topic modeling for untargeted substructure exploration in metabolomics
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Propagating annotations of molecular networks using in silico fragmentation
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Did a plant-herbivore arms race drive chemical diversity in Euphorbia?
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Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.
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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
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Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines
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Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption
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In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine
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Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose
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Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
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Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics
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Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages
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Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings
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Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy
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Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
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A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats
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The food metabolome: a window over dietary exposure
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Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols
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Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics
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A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes
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Implementations of the chemical structural and compositional similarity metric in R and Python
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Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
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A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
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The Metabolomics Society—Current State of the Membership and Future Directions
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
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MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
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Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli
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Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.
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Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
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MIBiG 2.0: a repository for biosynthetic gene clusters of known function
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Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
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The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
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Mass spectrometry searches using MASST
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Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
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Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication
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Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
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Linking genomics and metabolomics to chart specialized metabolic diversity
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Reproducible molecular networking of untargeted mass spectrometry data using GNPS
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Decomposing metabolite set activity levels with PALS
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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
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matchms - processing and similarity evaluation of mass spectrometry data
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
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BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
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matchms - processing and similarity evaluation of mass spectrometry data.
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ReDU: a framework to find and reanalyze public mass spectrometry data
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Feature-based molecular networking in the GNPS analysis environment
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Rapid Development of Improved Data-dependent Acquisition Strategies
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Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
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Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
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The ant fungus garden acts as an external digestive system
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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
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BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
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Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs
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Comparative Metabologenomics Analysis of Polar Actinomycetes
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Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
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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
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Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
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Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview
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Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
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Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery
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