Search Results - "Pieter Dorrestein"

Finding the Missing Links among Metabolites, Microbes, and the Host by Dorrestein, Pieter C., Mazmanian, Sarkis K., Knight, Rob

“…The unexpected diversity of the human microbiome and metabolome far exceeds the complexity of the human genome. Although we now understand microbial taxonomic…”
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Specialized Metabolites from the Microbiome in Health and Disease by Sharon, Gil, Garg, Neha, Debelius, Justine, Knight, Rob, Dorrestein, Pieter C., Mazmanian, Sarkis K.

“…The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development,…”
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ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs by Yang, Liuqing, Lin, Chunru, Liu, Wen, Zhang, Jie, Ohgi, Kenneth A., Grinstein, Jonathan D., Dorrestein, Pieter C., Rosenfeld, Michael G.

“…Although eukaryotic nuclei contain distinct architectural structures associated with noncoding RNAs (ncRNAs), their potential relationship to regulated…”
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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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The critical role that spectral libraries play in capturing the metabolomics community knowledge by Bittremieux, Wout, Wang, Mingxun, Dorrestein, Pieter C.

“…Background Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable…”
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Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation by Nothias, Louis-Félix, Nothias-Esposito, Mélissa, da Silva, Ricardo, Wang, Mingxun, Protsyuk, Ivan, Zhang, Zheng, Sarvepalli, Abi, Leyssen, Pieter, Touboul, David, Costa, Jean, Paolini, Julien, Alexandrov, Theodore, Litaudon, Marc, Dorrestein, Pieter C

“…It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s)…”
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Illuminating the dark matter in metabolomics by da Silva, Ricardo R., Dorrestein, Pieter C., Quinn, Robert A.

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The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases by Fogelson, Kelly A., Dorrestein, Pieter C., Zarrinpar, Amir, Knight, Rob

“…The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the…”
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra by Dührkop, Kai, Nothias, Louis-Félix, Fleischauer, Markus, Reher, Raphael, Ludwig, Marcus, Hoffmann, Martin A., Petras, Daniel, Gerwick, William H., Rousu, Juho, Dorrestein, Pieter C., Böcker, Sebastian

“…Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is…”
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Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy by Quinn, Robert A, Nothias, Louis-Felix, Vining, Oliver, Meehan, Michael, Esquenazi, Eduardo, Dorrestein, Pieter C

“…Molecular networking is a tandem mass spectrometry (MS/MS) data organizational approach that has been recently introduced in the drug discovery, metabolomics,…”
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Mass spectrometry-based metabolomics in microbiome investigations by Bauermeister, Anelize, Mannochio-Russo, Helena, Costa-Lotufo, Letícia V., Jarmusch, Alan K., Dorrestein, Pieter C.

“…Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as…”
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Dereplication of microbial metabolites through database search of mass spectra by Mohimani, Hosein, Gurevich, Alexey, Shlemov, Alexander, Mikheenko, Alla, Korobeynikov, Anton, Cao, Liu, Shcherbin, Egor, Nothias, Louis-Felix, Dorrestein, Pieter C., Pevzner, Pavel A.

“…Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products,…”
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Imaging mass spectrometry in microbiology by Dorrestein, Pieter C, Watrous, Jeramie D

“…Key Points Imaging mass spectrometry (IMS) provides atomic and/or molecular information in two dimensions and has the potential to characterize microorganisms…”
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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information by Dührkop, Kai, Fleischauer, Markus, Ludwig, Marcus, Aksenov, Alexander A., Melnik, Alexey V., Meusel, Marvin, Dorrestein, Pieter C., Rousu, Juho, Böcker, Sebastian

“…Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging…”
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Microbiome-wide association studies link dynamic microbial consortia to disease by Gilbert, Jack A., Quinn, Robert A., Debelius, Justine, Xu, Zhenjiang Z., Morton, James, Garg, Neha, Jansson, Janet K., Dorrestein, Pieter C., Knight, Rob

“…Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of…”
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High-confidence structural annotation of metabolites absent from spectral libraries by Hoffmann, Martin A., Nothias, Louis-Félix, Ludwig, Marcus, Fleischauer, Markus, Gentry, Emily C., Witting, Michael, Dorrestein, Pieter C., Dührkop, Kai, Böcker, Sebastian

“…Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched…”
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The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization by Molina-Santiago, Carlos, Pearson, John R., Navarro, Yurena, Berlanga-Clavero, María Victoria, Caraballo-Rodriguez, Andrés Mauricio, Petras, Daniel, García-Martín, María Luisa, Lamon, Gaelle, Haberstein, Birgit, Cazorla, Francisco M., de Vicente, Antonio, Loquet, Antoine, Dorrestein, Pieter C., Romero, Diego

“…Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these…”
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Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites by Li, Xuanji, Brejnrod, Asker Daniel, Ernst, Madeleine, Rykær, Martin, Herschend, Jakob, Olsen, Nanna Mee Coops, Dorrestein, Pieter C., Rensing, Christopher, Sørensen, Søren Johannes

“…Exposure to arsenic and cadmium is common. Epidemiological and animal studies have suggested that exposure to these two heavy metals can cause metabolic health…”
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Mass spectrometry of natural products: current, emerging and future technologies by Bouslimani, Amina, Sanchez, Laura M, Garg, Neha, Dorrestein, Pieter C

“…Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex…”
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NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products by Kim, Hyun Woo, Wang, Mingxun, Leber, Christopher A., Nothias, Louis-Félix, Reher, Raphael, Kang, Kyo Bin, van der Hooft, Justin J. J., Dorrestein, Pieter C., Gerwick, William H., Cottrell, Garrison W.

“…Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an…”
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