Propagating annotations of molecular networks using in silico fragmentation
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
Published in PLoS computational biology (01.04.2018)
Published in PLoS computational biology (01.04.2018)
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Journal Article
Comprehensive mass spectrometry‐guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
Kang, Kyo Bin, Ernst, Madeleine, Hooft, Justin J. J., Silva, Ricardo R., Park, Junha, Medema, Marnix H., Sung, Sang Hyun, Dorrestein, Pieter C.
Published in The Plant journal : for cell and molecular biology (01.06.2019)
Published in The Plant journal : for cell and molecular biology (01.06.2019)
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Journal Article
Illuminating the dark matter in metabolomics
da Silva, Ricardo R., Dorrestein, Pieter C., Quinn, Robert A.
Published in Proceedings of the National Academy of Sciences - PNAS (13.10.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (13.10.2015)
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Journal Article
Feature-based molecular networking in the GNPS analysis environment
Nothias, Louis-Félix, Petras, Daniel, Schmid, Robin, Dührkop, Kai, Rainer, Johannes, Sarvepalli, Abinesh, Protsyuk, Ivan, Ernst, Madeleine, Tsugawa, Hiroshi, Fleischauer, Markus, Aicheler, Fabian, Aksenov, Alexander A., Alka, Oliver, Allard, Pierre-Marie, Barsch, Aiko, Cachet, Xavier, Caraballo-Rodriguez, Andres Mauricio, Da Silva, Ricardo R., Dang, Tam, Garg, Neha, Gauglitz, Julia M., Gurevich, Alexey, Isaac, Giorgis, Jarmusch, Alan K., Kameník, Zdeněk, Kang, Kyo Bin, Kessler, Nikolas, Koester, Irina, Korf, Ansgar, Le Gouellec, Audrey, Ludwig, Marcus, Martin H., Christian, McCall, Laura-Isobel, McSayles, Jonathan, Meyer, Sven W., Mohimani, Hosein, Morsy, Mustafa, Moyne, Oriane, Neumann, Steffen, Neuweger, Heiko, Nguyen, Ngoc Hung, Nothias-Esposito, Melissa, Paolini, Julien, Phelan, Vanessa V., Pluskal, Tomáš, Quinn, Robert A., Rogers, Simon, Shrestha, Bindesh, Tripathi, Anupriya, van der Hooft, Justin J. J., Vargas, Fernando, Weldon, Kelly C., Witting, Michael, Yang, Heejung, Zhang, Zheng, Zubeil, Florian, Kohlbacher, Oliver, Böcker, Sebastian, Alexandrov, Theodore, Bandeira, Nuno, Wang, Mingxun, Dorrestein, Pieter C.
Published in Nature methods (01.09.2020)
Published in Nature methods (01.09.2020)
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Journal Article
Anthocyanin Profile of Elderberry Juice: A Natural-Based Bioactive Colouring Ingredient with Potential Food Application
da Silva, Ricardo F R, Barreira, João C M, Heleno, Sandrina A, Barros, Lillian, Calhelha, Ricardo C, Ferreira, Isabel C F R
Published in Molecules (Basel, Switzerland) (26.06.2019)
Published in Molecules (Basel, Switzerland) (26.06.2019)
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Journal Article
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols
Crüsemann, Max, O’Neill, Ellis C, Larson, Charles B, Melnik, Alexey V, Floros, Dimitrios J, da Silva, Ricardo R, Jensen, Paul R, Dorrestein, Pieter C, Moore, Bradley S
Published in Journal of natural products (Washington, D.C.) (24.03.2017)
Published in Journal of natural products (Washington, D.C.) (24.03.2017)
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Journal Article
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples
Melnik, Alexey V, da Silva, Ricardo R, Hyde, Embriette R, Aksenov, Alexander A, Vargas, Fernando, Bouslimani, Amina, Protsyuk, Ivan, Jarmusch, Alan K, Tripathi, Anupriya, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C
Published in Analytical chemistry (Washington) (18.07.2017)
Published in Analytical chemistry (Washington) (18.07.2017)
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Journal Article
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
Gauglitz, Julia M., Aceves, Christine M., Aksenov, Alexander A., Aleti, Gajender, Almaliti, Jehad, Bouslimani, Amina, Brown, Elizabeth A., Campeau, Anaamika, Caraballo-Rodríguez, Andrés Mauricio, Chaar, Rama, da Silva, Ricardo R., Demko, Alyssa M., Di Ottavio, Francesca, Elijah, Emmanuel, Ernst, Madeleine, Ferguson, L. Paige, Holmes, Xavier, Jarmusch, Alan K., Jiang, Lingjing, Kang, Kyo Bin, Koester, Irina, Kwan, Brian, Li, Jie, Li, Yueying, Melnik, Alexey V., Molina-Santiago, Carlos, Ni, Bohan, Oom, Aaron L., Panitchpakdi, Morgan W., Petras, Daniel, Quinn, Robert, Sikora, Nicole, Spengler, Katharina, Teke, Bahar, Tripathi, Anupriya, Ul-Hasan, Sabah, van der Hooft, Justin J.J., Vargas, Fernando, Vrbanac, Alison, Vu, Anthony Q., Wang, Steven C., Weldon, Kelly, Wilson, Kayla, Wozniak, Jacob M., Yoon, Michael, Bandeira, Nuno, Dorrestein, Pieter C.
Published in Food chemistry (01.01.2020)
Published in Food chemistry (01.01.2020)
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Journal Article
Lifestyle chemistries from phones for individual profiling
Bouslimani, Amina, Melnik, Alexey V., Xu, Zhenjiang, Amir, Amnon, da Silva, Ricardo R., Wang, Mingxun, Bandeira, Nuno, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C.
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2016)
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Journal Article
Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter
da Silva, Ricardo R., Vargas, Fernando, Ernst, Madeleine, Nguyen, Ngoc Hung, Bolleddu, Sanjana, del Rosario, Krizia Karen, Tsunoda, Shirley M., Dorrestein, Pieter C., Jarmusch, Alan K.
Published in Journal of the American Society for Mass Spectrometry (01.02.2019)
Published in Journal of the American Society for Mass Spectrometry (01.02.2019)
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Journal Article
Novel Pseudomonas Species Prevent the Growth of the Phytopathogenic Fungus Aspergillus flavus
Rabiço, Franciene, Borelli, Tiago Cabral, Alnoch, Robson Carlos, Polizeli, Maria de Lourdes Teixeira de Moraes, da Silva, Ricardo R, Silva-Rocha, Rafael, Guazzaroni, María-Eugenia
Published in Biotech (Basel) (30.03.2024)
Published in Biotech (Basel) (30.03.2024)
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Journal Article
Metabolic Profiling of Interspecies Interactions During Sessile Bacterial Cultivation Reveals Growth and Sporulation Induction in Paenibacillus amylolyticus in Response to Xanthomonas retroflexus
Herschend, Jakob, Ernst, Madeleine, Koren, Klaus, Melnik, Alexey V, da Silva, Ricardo R, Røder, Henriette L, Damholt, Zacharias B V, Hägglund, Per, Svensson, Birte, Sørensen, Søren J, Kühl, Michael, Dorrestein, Pieter C, Burmølle, Mette
Published in Frontiers in cellular and infection microbiology (29.03.2022)
Published in Frontiers in cellular and infection microbiology (29.03.2022)
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Journal Article
Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim
McAvoy, Andrew C, Jaiyesimi, Olakunle, Threatt, Paxton H, Seladi, Tyler, Goldberg, Joanna B, da Silva, Ricardo R, Garg, Neha
Published in ACS infectious diseases (08.05.2020)
Published in ACS infectious diseases (08.05.2020)
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Journal Article
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
Melnik, Alexey V., Vázquez-Baeza, Yoshiki, Aksenov, Alexander A., Hyde, Embriette, McAvoy, Andrew C., Wang, Mingxun, da Silva, Ricardo R., Protsyuk, Ivan, Wu, Jason V., Bouslimani, Amina, Lim, Yan Wei, Luzzatto-Knaan, Tal, Comstock, William, Quinn, Robert A., Wong, Richard, Humphrey, Greg, Ackermann, Gail, Spivey, Timothy, Brouha, Sharon S., Bandeira, Nuno, Lin, Grace Y., Rohwer, Forest, Conrad, Douglas J., Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C., Garg, Neha
Published in mSystems (24.09.2019)
Published in mSystems (24.09.2019)
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Journal Article
Evidence for internal field in graphite: a conduction electron spin-resonance study
Sercheli, M.S, Kopelevich, Y, Ricardo da Silva, R, Torres, J.H.S, Rettori, C
Published in Solid state communications (07.03.2002)
Published in Solid state communications (07.03.2002)
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Journal Article
Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication
Kang, Kyo Bin, Park, Eun Jin, da Silva, Ricardo R, Kim, Hyun Woo, Dorrestein, Pieter C, Sung, Sang Hyun
Published in Journal of natural products (Washington, D.C.) (24.08.2018)
Published in Journal of natural products (Washington, D.C.) (24.08.2018)
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Journal Article
Improving annotation propagation on molecular networks through random walks: introducing ChemWalker
Borelli, Tiago Cabral, Arini, Gabriel Santos, Feitosa, Luís G P, Dorrestein, Pieter C, Lopes, Norberto Peporine, da Silva, Ricardo R
Published in Bioinformatics (Oxford, England) (01.03.2023)
Published in Bioinformatics (Oxford, England) (01.03.2023)
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Journal Article
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung
Garg, Neha, Wang, Mingxun, Hyde, Embriette, da Silva, Ricardo R., Melnik, Alexey V., Protsyuk, Ivan, Bouslimani, Amina, Lim, Yan Wei, Wong, Richard, Humphrey, Greg, Ackermann, Gail, Spivey, Timothy, Brouha, Sharon S., Bandeira, Nuno, Lin, Grace Y., Rohwer, Forest, Conrad, Douglas J., Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C.
Published in Cell host & microbe (08.11.2017)
Published in Cell host & microbe (08.11.2017)
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Journal Article
In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation
Lee, Jiho, da Silva, Ricardo R., Jang, Hyeon Seok, Kim, Hyun Woo, Kwon, Yong Soo, Kim, Jung-Hwan, Yang, Heejung
Published in Food chemistry (15.10.2019)
Published in Food chemistry (15.10.2019)
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