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List of works by Justin J J van der Hooft

A community resource for paired genomic and metabolomic data mining

scientific article published in 2021

A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes

scientific article published in 2018

A comprehensive evaluation of the [2-14C](-)-epicatechin metabolome in rats.

scientific article

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

scientific article published on 02 April 2019

Absorption, metabolism, distribution and excretion of (-)-epicatechin: A review of recent findings

scientific article published on 7 November 2017

Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics

scientific article published on 19 November 2018

Advancements in capturing and mining mass spectrometry data are transforming natural products research

scientific article published on 09 October 2021

Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

scientific article published on 18 June 2021

An isotopic labeling approach linking natural products with biosynthetic gene clusters

scientific article published on 30 December 2021

Artificial intelligence for natural product drug discovery ⬇️

scientific article from 2023

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L

scientific article published on 02 July 2019

Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow

scientific article published on 12 February 2020

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

scientific article published on 09 November 2020

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

scientific article

Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea.

scientific article published on 31 May 2013

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

scientific article published on 28 September 2021

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

scientific article published in January 2021

Chemical Gradients of Plant Substrates in an <i>Atta texana</i> Fungus Garden

scientific article published on 03 August 2021

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

scientific article published on 16 November 2020

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

scientific article published on 5 May 2020

Combining Feature-Based Molecular Networking and Contextual Mass Spectral Libraries to Decipher Nutrimetabolomics Profiles

scientific article published on 21 October 2022

Comparative Metabologenomics Analysis of Polar Actinomycetes

scientific article published in 2021

Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules

scientific article published in 2022

Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery

scientific article published in 2021

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

scientific article published on 25 March 2019

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

scientific article published on 7 November 2018

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

scientific article

Computational Metabolomics Tools Reveal Metabolic Reconfigurations Underlying the Effects of Biostimulant Seaweed Extracts on Maize Plants under Drought Stress Conditions

scientific article published in 2022

Data mining and visualisation: general discussion

scientific article published on 01 August 2019

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

scientific article published on 9 December 2018

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra

scientific article published on 01 August 2019

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

scientific article published on 15 May 2018

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines

scientific article

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching

scientific article published on 23 January 2023

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching

scientific article published on 29 June 2022

FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data

scientific article published on 22 December 2022

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

From mass spectral features to molecules in molecular networks: a novel workflow for untargeted metabolomics

scientific article published on 22 December 2021

Future challenges and new approaches: general discussion

scientific article published on 01 August 2019

Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools

scientific article published on 5 December 2022

High resolution techniques: general discussion

scientific article published on 01 August 2019

Homologue series detection and management in LC-MS data with homologueDiscoverer

scientific article published on 15 November 2022

Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols

scientific article published on 30 October 2013

Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes

scientific article

Implementations of the chemical structural and compositional similarity metric in R and Python

scientific article published on 11 February 2019

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics

scientific article published on 09 October 2019

In silico prediction and automatic LC-MS(n) annotation of green tea metabolites in urine

scientific article

Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi

scientific article published on 20 December 2011

Integrative omics approaches for biosynthetic pathway discovery in plants

scientific article published in January 2022

Interactions of black tea polyphenols with human gut microbiota: implications for gut and cardiovascular health.

scientific article published on 30 October 2013

Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae)

article

Linking genomics and metabolomics to chart specialized metabolic diversity

scientific article published on 12 May 2020

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

scientific article published on 01 January 2020

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

scientific article published on 18 November 2022

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

scientific article published on 9 December 2024

MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra

chemical compound

MS2Query: reliable and scalable MS mass spectra-based analogue search

scientific article published on 29 March 2023

Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Strains

scientific article published in 2022

Mass spectrometry searches using MASST

scientific article published on 01 January 2020

Metabolic interactions shape a community's phenotype

scientific article published in 2022

Metabolite Identification Using Automated Comparison of High-Resolution Multistage Mass Spectral Trees

scientific article

Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy

scientific article published in 2017

Metabolome-guided genome mining of RiPP natural products

scientific article published in August 2023

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

scientific article

Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication

scientific article published on 11 March 2020

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

scientific article published on 16 July 2019

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

scientific article published on 31 May 2019

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry.

scientific article published on 14 September 2017

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

scientific article published on 20 October 2021

NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

scientific article published on 6 October 2021

Non-smoky glycosyltransferase1 prevents the release of smoky aroma from tomato fruit.

scientific article published on 16 August 2013

Orange juice (poly)phenols are highly bioavailable in humans

scientific article published on 27 August 2014

Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking

scientific article published on 20 July 2020

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation

scientific article published on 9 December 2010

Propagating annotations of molecular networks using in silico fragmentation

scientific article published on 18 April 2018

Ranking Metabolite Sets by Their Activity Levels

scientific article

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions

scientific article published in 2021

Rapid Development of Improved Data-Dependent Acquisition Strategies

scientific article published in 2021

Rapid and sustained systemic circulation of conjugated gut microbial catabolites after single-dose black tea extract consumption

scientific article published on 10 April 2014

ReDU: a framework to find and reanalyze public mass spectrometry data

scientific article published on 17 August 2020

Recent advances in mass spectrometry-based computational metabolomics

Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS

scholarly article published 8 August 2019

Reproducible mass spectrometry data processing and compound annotation in MZmine 3

scientific article published on 20 May 2024

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

scientific article published on 13 May 2020

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Simulated-to-real Benchmarking of Acquisition Methods in Metabolomics

scientific article published on 15 January 2023

Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics

scientific article published in 2023

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Spectral trees as a robust annotation tool in LC–MS based metabolomics

Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts

scientific article published on 12 April 2012

Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake

scientific article published on 2 August 2012

Structural elucidation of low abundant metabolites in complex sample matrices

Substantial Extracellular Metabolic Differences Found Between Phylogenetically Closely Related Probiotic and Pathogenic Strains of

scientific article published on 19 February 2019

Substructure-based annotation of high-resolution multistage MS(n) spectral trees

scientific article published in October 2012

The Metabolomics Society-Current State of the Membership and Future Directions

scientific article published on 03 May 2019

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

scientific article published on 14 November 2019

The food metabolome: a window over dietary exposure

scientific article

Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma -derived metabolite cues

scientific article published on 13 November 2022

Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose

article

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics

scientific article

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

scientific article published on 15 June 2018

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages

scientific article published on 30 July 2019

Updates in metabolomics tools and resources: 2014-2015.

scientific article published on 14 October 2015

Urinary antihypertensive drug metabolite screening using molecular networking coupled to high-resolution mass spectrometry fragmentation

scientific article published on 05 July 2016

Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs

scientific article published on 03 November 2020

ants promote fungus garden hygiene using -derived metabolite cues

scientific article published on 20 June 2023

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

scientific article published in February 2023

matchms - processing and similarity evaluation of mass spectrometry data.

scientific article published on 31 August 2020

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