MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
Florian Huber
Sven van der Burg
Justin J.J. van der Hooft
Lars Ridder
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
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
Sven van der Burg
van der Burg Sven
ORCID: 0000-0003-1250-6968
Neural Representation of Motor Output, Context and Behavioral Adaptation in Rat Medial Prefrontal Cortex During Learned Behavior
10.3389/fncir.2018.00075
Visual stimulus-specific habituation of innate defensive behaviour in mice
10.1242/jeb.230433
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
10.1101/2021.04.18.440324
