Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
Grímur Hjörleifsson Eldjárn
Niranjan Nagarajan
Andrew Ramsay
Justin J. J. van der Hooft
Katherine R. Duncan
Sylvia Soldatou
Juho Rousu
Rónán Daly
Joe Wandy
Simon Rogers
PLOS Computational Biology, 2021-5-4
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
10.1007/s10994-016-5618-0
Predicting Protein Producibility in Filamentous Fungi
10.1101/138560
Principal Metabolic Flux Mode Analysis
10.1101/163055
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
10.1371/journal.pcbi.1005678
Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models
10.3390/metabo9080160
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
10.1101/2020.09.02.278986
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
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
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1101/2020.08.11.245928
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
ReDU: a framework to find and reanalyze public mass spectrometry data
10.1038/s41592-020-0916-7
Feature-based molecular networking in the GNPS analysis environment
10.1038/s41592-020-0933-6
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
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
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
10.1093/gigascience/giaa154
Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs
10.1371/journal.ppat.1008932
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
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
10.1101/2021.04.18.440324
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
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
Rónán Daly
Daly Rónán
ORCID: 0000-0002-1275-6820
Email: ronan.daly@glasgow.ac.uk
Metabolomics Identifies Multiple Candidate Biomarkers to Diagnose and Stage Human African Trypanosomiasis
10.1371/journal.pntd.0005140
MetaboCraft: building a Minecraft plugin for metabolomics
10.1093/bioinformatics/bty102
ShinyKGode: an interactive application for ODE parameter inference using gradient matching
10.1093/bioinformatics/bty089
Plasma Itaconate elevation following successful cDMARD treatment in early rheumatoid arthritis patients elucidates disease activity associated macrophage activation
10.1101/19001594
Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses
10.1098/rspb.2019.2109
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.1101/744227
Decomposing metabolite set activity levels with PALS
10.1101/2020.06.07.138974
Changes in Plasma Itaconate Elevation in Early Rheumatoid Arthritis Patients Elucidates Disease Activity Associated Macrophage Activation
10.3390/metabo10060241
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
R package for statistical inference in dynamical systems using kernel based gradient matching: KGode
10.1007/s00180-020-01014-x
A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection
10.1038/s41378-021-00243-4
High sodium intake, glomerular hyperfiltration, and protein catabolism in patients with essential hypertension
10.1093/cvr/cvaa205
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
Katherine R. Duncan
Duncan Katherine R.
/ Katherine Duncan
ORCID: 0000-0002-3670-4849
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from salinispora species
10.1016/j.chembiol.2015.03.010
Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada
10.1007/s10295-014-1529-x
Bioprospecting from marine sediments of New Brunswick, Canada
10.3390/md12020899
An integrative approach to decipher the chemical antagonism between the competing endophytes paraconiothyrium variabile and Bacillus subtilis
10.1021/acs.jnatprod.6b01185
Chemical dereplication of marine actinomycetes by liquid chromatography-high resolution mass spectrometry profiling and statistical analysis
10.1016/j.aca.2013.10.029
Antagonistic interactions mediated by marine bacteria
10.1007/s10886-013-0316-x
Using molecular networking for microbial secondary metabolite bioprospecting
10.3390/metabo6010002
Competitive strategies differentiate closely related species of marine actinobacteria
10.1038/ismej.2015.128
Temperature driven changes in benthic bacterial diversity influences biogeochemical cycling in coastal sediments
10.3389/fmicb.2018.01730
Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery
10.1093/femsle/fnz142
Awakening ancient polar actinobacteria
10.1099/mic.0.000845
The Natural Products Atlas
10.1021/acscentsci.9b00806
Bioassay- and metabolomics-guided screening of bioactive soil actinomycetes from the ancient city of Ihnasia, Egypt
10.1371/journal.pone.0226959
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics
10.3390/microorganisms9020311
Comparative metabologenomics analysis of polar actinomycetes
10.3390/md19020103
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
