Search Results - "Silva, Ricardo R"

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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Feature-based molecular networking in the GNPS analysis environment by 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.

“…Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based…”
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Comprehensive mass spectrometry‐guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae by Kang, Kyo Bin, Ernst, Madeleine, Hooft, Justin J. J., Silva, Ricardo R., Park, Junha, Medema, Marnix H., Sung, Sang Hyun, Dorrestein, Pieter C.

“…Summary Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped…”
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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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Improved virus purification processes for vaccines and gene therapy by Nestola, Piergiuseppe, Peixoto, Cristina, Silva, Ricardo R. J. S, Alves, Paula M., Mota, José P. B., Carrondo, Manuel J. T.

“…ABSTRACT The downstream processing of virus particles for vaccination or gene therapy is becoming a critical bottleneck as upstream titers keep improving…”
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Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells by Dos Santos, Ancély F., Inague, Alex, Arini, Gabriel S., Terra, Letícia F., Wailemann, Rosangela A. M., Pimentel, André C., Yoshinaga, Marcos Y., Silva, Ricardo R., Severino, Divinomar, de Almeida, Daria Raquel Q., Gomes, Vinícius M., Bruni-Cardoso, Alexandre, Terra, Walter R., Miyamoto, Sayuri, Baptista, Maurício S., Labriola, Leticia

“…Lack of effective treatments for aggressive breast cancer is still a major global health problem. We have previously reported that photodynamic therapy using…”
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Combination of GC-MS Molecular Networking and Larvicidal Effect against Aedes aegypti for the Discovery of Bioactive Substances in Commercial Essential Oils by Pilon, Alan Cesar, Del Grande, Marcelo, Silvério, Maíra R S, Silva, Ricardo R, Albernaz, Lorena C, Vieira, Paulo Cézar, Lopes, João Luis Callegari, Espindola, Laila S, Lopes, Norberto Peporine

“…Dengue is a neglected disease, present mainly in tropical countries, with more than 5.2 million cases reported in 2019. Vector control remains the most…”
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Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols by 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

“…In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery…”
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Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples by 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

“…Increasing appreciation of the gut microbiome’s role in health motivates understanding the molecular composition of human feces. To analyze such complex…”
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Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages by 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.

“…•First large-scale food composition analysis using mass spectral molecular networking.•A methodological pipeline for compound discovery applicable to diverse…”
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Lifestyle chemistries from phones for individual profiling by Bouslimani, Amina, Melnik, Alexey V., Xu, Zhenjiang, Amir, Amnon, da Silva, Ricardo R., Wang, Mingxun, Bandeira, Nuno, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C.

“…Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the…”
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Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter by 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.

“…Polymers are a common component of chemical background which complicates data analysis and can impair interpretation. Undesired chemical background cannot…”
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Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L by Ernst, Madeleine, Nothias, Louis-Félix, van der Hooft, Justin J J, Silva, Ricardo R, Saslis-Lagoudakis, C Haris, Grace, Olwen M, Martinez-Swatson, Karen, Hassemer, Gustavo, Funez, Luís A, Simonsen, Henrik T, Medema, Marnix H, Staerk, Dan, Nilsson, Niclas, Lovato, Paola, Dorrestein, Pieter C, Rønsted, Nina

“…Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic…”
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Metabolomics Analysis of Bacterial Pathogen Burkholderia thailandensis and Mammalian Host Cells in Co-culture by Aiosa, Nicole, Sinha, Anupama, Jaiyesimi, Olakunle A., da Silva, Ricardo R., Branda, Steven S., Garg, Neha

“…The Tier 1 HHS/USDA Select Agent Burkholderia pseudomallei is a bacterial pathogen that is highly virulent when introduced into the respiratory tract and…”
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Anthocyanin Profile of Elderberry Juice: A Natural-Based Bioactive Colouring Ingredient with Potential Food Application by da Silva, Ricardo F R, Barreira, João C M, Heleno, Sandrina A, Barros, Lillian, Calhelha, Ricardo C, Ferreira, Isabel C F R

“…Elderberry ( L.) is a widely disseminated plant that produces bright black berries containing high quantities of anthocyanins, acknowledged for their…”
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Rosemary ( Rosmarinus officinalis L.) Glycolic Extract Protects Liver Mitochondria from Oxidative Damage and Prevents Acetaminophen-Induced Hepatotoxicity by Guimarães, Natalia S S, Ramos, Vyctória S, Prado-Souza, Laura F L, Lopes, Rayssa M, Arini, Gabriel S, Feitosa, Luís G P, Silva, Ricardo R, Nantes, Iseli L, Damasceno, Debora C, Lopes, Norberto P, Rodrigues, Tiago

“…L. (rosemary) is an aromatic culinary herb. Native to the Mediterranean region, it is currently cultivated worldwide. In addition to its use as a condiment in…”
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Novel Pseudomonas Species Prevent the Growth of the Phytopathogenic Fungus Aspergillus flavus by 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

“…In response to the escalating demand for sustainable agricultural methodologies, the utilization of microbial volatile organic compounds (VOCs) as antagonists…”
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Metabolic Profiling of Interspecies Interactions During Sessile Bacterial Cultivation Reveals Growth and Sporulation Induction in Paenibacillus amylolyticus in Response to Xanthomonas retroflexus by 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

“…The toolbox available for microbiologists to study interspecies interactions is rapidly growing, and with continuously more advanced instruments, we are able…”
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Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim by McAvoy, Andrew C, Jaiyesimi, Olakunle, Threatt, Paxton H, Seladi, Tyler, Goldberg, Joanna B, da Silva, Ricardo R, Garg, Neha

“…The Burkholderia cepacia complex is a group of closely related bacterial species with large genomes that infect immunocompromised individuals and those living…”
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking by Wang, Mingxun, Carver, Jeremy J, Garg, Neha, Peng, Yao, Nguyen, Don Duy, Watrous, Jeramie, Kapono, Clifford A, Luzzatto-Knaan, Tal, Bouslimani, Amina, Melnik, Alexey V, Meehan, Michael J, Liu, Wei-Ting, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Quinn, Robert A, Hsu, Cheng-Chih, Floros, Dimitrios J, Gavilan, Ronnie G, Kleigrewe, Karin, Northen, Trent, Parrot, Delphine, Carlson, Erin E, Aigle, Bertrand, Jelsbak, Lars, Pevzner, Pavel, Edlund, Anna, McLean, Jeffrey, Piel, Jörn, Gerwick, Lena, Liaw, Chih-Chuang, Yang, Yu-Liang, Humpf, Hans-Ulrich, Maansson, Maria, Keyzers, Robert A, Sims, Amy C, Johnson, Andrew R, Sidebottom, Ashley M, Klitgaard, Andreas, Larson, Charles B, Boya P, Cristopher A, Torres-Mendoza, Daniel, Gonzalez, David J, Silva, Denise B, Marques, Lucas M, Demarque, Daniel P, Pociute, Egle, O'Neill, Ellis C, Briand, Enora, Helfrich, Eric J N, Ryffel, Florian, Houson, Hailey, Mohimani, Hosein, Zeng, Yi, Vorholt, Julia A, Kurita, Kenji L, Charusanti, Pep, McPhail, Kerry L, Vuong, Lisa, Elfeki, Maryam, Traxler, Matthew F, Engene, Niclas, Koyama, Nobuhiro, Vining, Oliver B, Baric, Ralph, Tomasi, Sophie, Jenkins, Stefan, Hoffman, Thomas, Williams, Philip G, Dai, Jingqui, Neupane, Ram, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Pogliano, Kit, Linington, Roger G, Moore, Bradley S, Dorrestein, Pieter C

“…GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of…”
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