Search Results - "van der Hooft, Justin J. J."

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 by Wolfender, Jean-Luc, Nuzillard, Jean-Marc, van der Hooft, Justin J. J, Renault, Jean-Hugues, Bertrand, Samuel

“…The rapid innovations in metabolite profiling, bioassays and chemometrics have led to a paradigm shift in natural product (NP) research. Indeed, having partial…”
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Linking genomics and metabolomics to chart specialized metabolic diversity by van der Hooft, Justin J J, Mohimani, Hosein, Bauermeister, Anelize, Dorrestein, Pieter C, Duncan, Katherine R, Medema, Marnix H

“…Microbial and plant specialized metabolites constitute an immense chemical diversity, and play key roles in mediating ecological interactions between…”
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MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra by Huber, Florian, van der Burg, Sven, van der Hooft, Justin J. J., Ridder, Lars

“…Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are…”
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Propagating annotations of molecular networks using in silico fragmentation by da Silva, Ricardo R, Wang, Mingxun, Nothias, Louis-Félix, van der Hooft, Justin J J, Caraballo-Rodríguez, Andrés Mauricio, Fox, Evan, Balunas, Marcy J, Klassen, Jonathan L, Lopes, Norberto Peporine, Dorrestein, Pieter C

“…The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological…”
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Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols by Clifford, Michael N, van der Hooft, Justin JJ, Crozier, Alan

“…Recent research on the bioavailability of flavan-3-ols after ingestion of green tea by humans is reviewed. Glucuronide, sulfate, and methyl metabolites of…”
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra by Rogers, Simon, Ong, Cher Wei, Wandy, Joe, Ernst, Madeleine, Ridder, Lars, van der Hooft, Justin J J

“…Complex metabolite mixtures are challenging to unravel. Mass spectrometry (MS) is a widely used and sensitive technique for obtaining structural information of…”
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics by Wandy, Joe, Davies, Vinny, J. J. van der Hooft, Justin, Weidt, Stefan, Daly, Rónán, Rogers, Simon

“…Liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) is widely used in identifying small molecules in untargeted metabolomics. Various…”
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Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions by Hjörleifsson Eldjárn, Grímur, Ramsay, Andrew, van der Hooft, Justin J J, Duncan, Katherine R, Soldatou, Sylvia, Rousu, Juho, Daly, Rónán, Wandy, Joe, Rogers, Simon

“…Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired…”
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iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures by Louwen, Joris J R, Kautsar, Satria A, van der Burg, Sven, Medema, Marnix H, van der Hooft, Justin J J

“…Microbial specialised metabolism is full of valuable natural products that are applied clinically, agriculturally, and industrially. The genes that encode…”
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Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches by Beniddir, Mehdi A, Kang, Kyo Bin, Genta-Jouve, Grégory, Huber, Florian, Rogers, Simon, van der Hooft, Justin J J

“…Covering: up to the end of 2020Recently introduced computational metabolome mining tools have started to positively impact the chemical and biological…”
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Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs by Giordani, Federica, Paape, Daniel, Vincent, Isabel M, Pountain, Andrew W, Fernández-Cortés, Fernando, Rico, Eva, Zhang, Ning, Morrison, Liam J, Freund, Yvonne, Witty, Michael J, Peter, Rosemary, Edwards, Darren Y, Wilkes, Jonathan M, van der Hooft, Justin J J, Regnault, Clément, Read, Kevin D, Horn, David, Field, Mark C, Barrett, Michael P

“…Livestock diseases caused by Trypanosoma congolense, T. vivax and T. brucei, collectively known as nagana, are responsible for billions of dollars in lost food…”
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Rapid Development of Improved Data-Dependent Acquisition Strategies by Davies, Vinny, Wandy, Joe, Weidt, Stefan, van der Hooft, Justin J. J, Miller, Alice, Daly, Rónán, Rogers, Simon

“…Tandem mass spectrometry (LC-MS/MS) is widely used to identify unknown ions in untargeted metabolomics. Data-dependent acquisition (DDA) chooses which ions to…”
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Advancements in capturing and mining mass spectrometry data are transforming natural products research by Jarmusch, Scott A, van der Hooft, Justin J J, Dorrestein, Pieter C, Jarmusch, Alan K

“…Covering: 2016 up to 2021Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key…”
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships by Huber, Florian, Ridder, Lars, Verhoeven, Stefan, Spaaks, Jurriaan H, Diblen, Faruk, Rogers, Simon, van der Hooft, Justin J J

“…Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching…”
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Integrative omics approaches for biosynthetic pathway discovery in plants by Singh, Kumar Saurabh, van der Hooft, Justin J J, van Wees, Saskia C M, Medema, Marnix H

“…Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic…”
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MS2Query: reliable and scalable MS2 mass spectra-based analogue search by de Jonge, Niek F., Louwen, Joris J. R., Chekmeneva, Elena, Camuzeaux, Stephane, Vermeir, Femke J., Jansen, Robert S., Huber, Florian, van der Hooft, Justin J. J.

“…Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge of metabolite annotation and identification. Only few metabolites…”
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Combining Feature-Based Molecular Networking and Contextual Mass Spectral Libraries to Decipher Nutrimetabolomics Profiles by Renai, Lapo, Ulaszewska, Marynka, Mattivi, Fulvio, Bartoletti, Riccardo, Del Bubba, Massimo, van der Hooft, Justin J. J.

“…Untargeted metabolomics approaches deal with complex data hindering structural information for the comprehensive analysis of unknown metabolite features. We…”
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Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics by van der Hooft, Justin J. J, Wandy, Joe, Young, Francesca, Padmanabhan, Sandosh, Gerasimidis, Konstantinos, Burgess, Karl E. V, Barrett, Michael P, Rogers, Simon

“…In untargeted metabolomics approaches, the inability to structurally annotate relevant features and map them to biochemical pathways is hampering the full…”
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Interactions of black tea polyphenols with human gut microbiota: implications for gut and cardiovascular health by van Duynhoven, John, Vaughan, Elaine E, van Dorsten, Ferdi, Gomez-Roldan, Victoria, de Vos, Ric, Vervoort, Jacques, van der Hooft, Justin JJ, Roger, Laure, Draijer, Richard, Jacobs, Doris M

“…Epidemiologic studies have convincingly associated consumption of black tea with reduced cardiovascular risk. Research on the bioactive molecules has…”
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A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters by Witjes, Lotte, Kooke, Rik, van der Hooft, Justin J J, de Vos, Ric C H, Keurentjes, Joost J B, Medema, Marnix H, Nijveen, Harm

“…Plants produce a plethora of specialized metabolites to defend themselves against pathogens and insects, to attract pollinators and to communicate with other…”
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