Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Beghini, Francesco, McIver, Lauren J, Blanco-Míguez, Aitor, Dubois, Leonard, Asnicar, Francesco, Maharjan, Sagun, Mailyan, Ana, Manghi, Paolo, Scholz, Matthias, Thomas, Andrew Maltez, Valles-Colomer, Mireia, Weingart, George, Zhang, Yancong, Zolfo, Moreno, Huttenhower, Curtis, Franzosa, Eric A, Segata, Nicola
Published in eLife (04.05.2021)
Published in eLife (04.05.2021)
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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Asnicar, Francesco, Thomas, Andrew Maltez, Beghini, Francesco, Mengoni, Claudia, Manara, Serena, Manghi, Paolo, Zhu, Qiyun, Bolzan, Mattia, Cumbo, Fabio, May, Uyen, Sanders, Jon G., Zolfo, Moreno, Kopylova, Evguenia, Pasolli, Edoardo, Knight, Rob, Mirarab, Siavash, Huttenhower, Curtis, Segata, Nicola
Published in Nature communications (19.05.2020)
Published in Nature communications (19.05.2020)
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Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
Tarallo, Sonia, Ferrero, Giulio, Gallo, Gaetano, Francavilla, Antonio, Clerico, Giuseppe, Realis Luc, Alberto, Manghi, Paolo, Thomas, Andrew Maltez, Vineis, Paolo, Segata, Nicola, Pardini, Barbara, Naccarati, Alessio, Cordero, Francesca
Published in mSystems (17.09.2019)
Published in mSystems (17.09.2019)
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Dysregulation of the PRUNE2/PCA3 genetic axis in human prostate cancer: from experimental discovery to validation in two independent patient cohorts
Lauer, Richard C, Barry, Marc, Smith, Tracey L, Thomas, Andrew Maltez, Wu, Jin, Du, Ruofei, Lee, Ji-Hyun, Rao, Arpit, Dobroff, Andrey S, Arap, Marco A, Nunes, Diana N, Silva, Israel T, Dias-Neto, Emmanuel, Chen, Isan, McCance, Dennis J, Cavenee, Webster K, Pasqualini, Renata, Arap, Wadih
Published in eLife (16.01.2023)
Published in eLife (16.01.2023)
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Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
Asnicar, Francesco, Berry, Sarah E., Valdes, Ana M., Nguyen, Long H., Piccinno, Gianmarco, Drew, David A., Leeming, Emily, Gibson, Rachel, Le Roy, Caroline, Khatib, Haya Al, Francis, Lucy, Mazidi, Mohsen, Mompeo, Olatz, Valles-Colomer, Mireia, Tett, Adrian, Beghini, Francesco, Dubois, Léonard, Bazzani, Davide, Thomas, Andrew Maltez, Mirzayi, Chloe, Khleborodova, Asya, Oh, Sehyun, Hine, Rachel, Bonnett, Christopher, Capdevila, Joan, Danzanvilliers, Serge, Giordano, Francesca, Geistlinger, Ludwig, Waldron, Levi, Davies, Richard, Hadjigeorgiou, George, Wolf, Jonathan, Ordovás, José M., Gardner, Christopher, Franks, Paul W., Chan, Andrew T., Huttenhower, Curtis, Spector, Tim D., Segata, Nicola
Published in Nature medicine (01.02.2021)
Published in Nature medicine (01.02.2021)
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Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
Thomas, Andrew Maltez, Manghi, Paolo, Asnicar, Francesco, Pasolli, Edoardo, Armanini, Federica, Zolfo, Moreno, Beghini, Francesco, Manara, Serena, Karcher, Nicolai, Pozzi, Chiara, Gandini, Sara, Serrano, Davide, Tarallo, Sonia, Francavilla, Antonio, Gallo, Gaetano, Trompetto, Mario, Ferrero, Giulio, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Wirbel, Jakob, Schrotz-King, Petra, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg, Cordero, Francesca, Dias-Neto, Emmanuel, Setubal, João Carlos, Tett, Adrian, Pardini, Barbara, Rescigno, Maria, Waldron, Levi, Naccarati, Alessio, Segata, Nicola
Published in Nature medicine (01.04.2019)
Published in Nature medicine (01.04.2019)
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Journal Article
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
Lee, Karla A., Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus, Derosa, Lisa, Dhomen, Nathalie, Brooks, Kelly, Harland, Mark, Harries, Mark, Leeming, Emily R., Lorigan, Paul, Manghi, Paolo, Marais, Richard, Newton-Bishop, Julia, Nezi, Luigi, Pinto, Federica, Potrony, Miriam, Puig, Susana, Serra-Bellver, Patricio, Shaw, Heather M., Tamburini, Sabrina, Valpione, Sara, Vijay, Amrita, Waldron, Levi, Zitvogel, Laurence, Zolfo, Moreno, de Vries, Elisabeth G. E., Nathan, Paul, Fehrmann, Rudolf S. N., Bataille, Véronique, Hospers, Geke A. P., Spector, Tim D., Weersma, Rinse K., Segata, Nicola
Published in Nature medicine (01.03.2022)
Published in Nature medicine (01.03.2022)
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Journal Article
Correction for Tarallo et al., "Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples"
Tarallo, Sonia, Ferrero, Giulio, Gallo, Gaetano, Francavilla, Antonio, Clerico, Giuseppe, Realis Luc, Alberto, Manghi, Paolo, Thomas, Andrew Maltez, Vineis, Paolo, Segata, Nicola, Pardini, Barbara, Naccarati, Alessio, Cordero, Francesca
Published in mSystems (18.02.2020)
Published in mSystems (18.02.2020)
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Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
Terrisse, Safae, Derosa, Lisa, Iebba, Valerio, Ghiringhelli, François, Vaz-Luis, Ines, Kroemer, Guido, Fidelle, Marine, Christodoulidis, Stergios, Segata, Nicola, Thomas, Andrew Maltez, Martin, Anne-Laure, Sirven, Aude, Everhard, Sibille, Aprahamian, Fanny, Nirmalathasan, Nitharsshini, Aarnoutse, Romy, Smidt, Marjolein, Ziemons, Janine, Caldas, Carlos, Loibl, Sibylle, Denkert, Carsten, Durand, Sylvere, Iglesias, Claudia, Pietrantonio, Filippo, Routy, Bertrand, André, Fabrice, Pasolli, Edoardo, Delaloge, Suzette, Zitvogel, Laurence
Published in Cell death and differentiation (01.09.2021)
Published in Cell death and differentiation (01.09.2021)
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Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics
Antunes, Luciana Principal, Martins, Layla Farage, Pereira, Roberta Verciano, Thomas, Andrew Maltez, Barbosa, Deibs, Lemos, Leandro Nascimento, Silva, Gianluca Major Machado, Moura, Livia Maria Silva, Epamino, George Willian Condomitti, Digiampietri, Luciano Antonio, Lombardi, Karen Cristina, Ramos, Patricia Locosque, Quaggio, Ronaldo Bento, de Oliveira, Julio Cezar Franco, Pascon, Renata Castiglioni, Cruz, João Batista da, da Silva, Aline Maria, Setubal, João Carlos
Published in Scientific reports (12.12.2016)
Published in Scientific reports (12.12.2016)
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Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma
Björk, Johannes R., Bolte, Laura A., Maltez Thomas, Andrew, Lee, Karla A., Rossi, Niccolo, Wind, Thijs T., Smit, Lotte M., Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus, Derosa, Lisa, Dhomen, Nathalie, Brooks, Kelly, Harland, Mark, Harries, Mark, Lorigan, Paul, Manghi, Paolo, Marais, Richard, Newton-Bishop, Julia, Nezi, Luigi, Pinto, Federica, Potrony, Miriam, Puig, Susana, Serra-Bellver, Patricio, Shaw, Heather M., Tamburini, Sabrina, Valpione, Sara, Waldron, Levi, Zitvogel, Laurence, Zolfo, Moreno, de Vries, Elisabeth G. E., Nathan, Paul, Fehrmann, Rudolf S. N., Spector, Tim D., Bataille, Véronique, Segata, Nicola, Hospers, Geke A. P., Weersma, Rinse K.
Published in Nature medicine (01.03.2024)
Published in Nature medicine (01.03.2024)
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Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission
Al Assal, Karina, Prifti, Edi, Belda, Eugeni, Sala, Priscila, Clément, Karine, Dao, Maria-Carlota, Doré, Joel, Levenez, Florence, Taddei, Carla R, Fonseca, Danielle Cristina, Rocha, Ilanna Marques, Balmant, Bianca Depieri, Thomas, Andrew Maltez, Santo, Marco A, Dias-Neto, Emmanuel, Setubal, João Carlos, Zucker, Jean-Daniel, Belarmino, Giliane, Torrinhas, Raquel Susana, Waitzberg, Dan L
Published in Nutrients (21.01.2020)
Published in Nutrients (21.01.2020)
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Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms
Thomas, Andrew Maltez, Gleber-Netto, Frederico Omar, Fernandes, Gustavo Ribeiro, Amorim, Maria, Barbosa, Luisa Fernanda, Francisco, Ana Lúcia Noronha, de Andrade, Arthur Guerra, Setubal, João Carlos, Kowalski, Luiz Paulo, Nunes, Diana Noronha, Dias-Neto, Emmanuel
Published in BMC microbiology (03.10.2014)
Published in BMC microbiology (03.10.2014)
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Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism
Sato, Fabio Takeo, Yap, Yu Anne, Crisma, Amanda Rabello, Portovedo, Mariana, Murata, Gilson Masahiro, Hirabara, Sandro Massao, Ribeiro, Willian Rodrigues, Marcantonio Ferreira, Caroline, Cruz, Maysa Mariana, Pereira, Joice Naiara Bertaglia, Payolla, Tanyara Baliani, Guima, Suzana Eiko Sato, Thomas, Andrew Maltez, Setubal, João Carlos, Alonso-Vale, Maria Isabel Cardoso, Santos, Marinilce Fagundes, Curi, Rui, Marino, Eliana, Vinolo, Marco A R
Published in Cells (Basel, Switzerland) (01.09.2020)
Published in Cells (Basel, Switzerland) (01.09.2020)
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Circulating inflammatory proteins associate with response to immune checkpoint inhibition therapy in patients with advanced melanoma
Rossi, Niccolò, Lee, Karla A., Bermudez, Maria V., Visconti, Alessia, Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Newton-Bishop, Julia, Harland, Mark, Shaw, Heather M., Harries, Mark, Sacco, Joseph, Board, Ruth, Lorigan, Paul, de Vries, Elisabeth G.E., Segata, Nicola, Taams, Leonie, Papa, Sophie, Spector, Tim D., Nathan, Paul, Weersma, Rinse K., Hospers, Geke A.P., Fehrmann, Rudolf S.N., Bataille, Veronique, Falchi, Mario
Published in EBioMedicine (01.09.2022)
Published in EBioMedicine (01.09.2022)
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Comparative Metagenomics
Maltez Thomas, Andrew, Prata Lima, Felipe, Maria Silva Moura, Livia, Maria da Silva, Aline, Dias-Neto, Emmanuel, Setubal, João C
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2018)
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2018)
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Journal Article
Machine learning for microbiologists
Asnicar, Francesco, Thomas, Andrew Maltez, Passerini, Andrea, Waldron, Levi, Segata, Nicola
Published in Nature reviews. Microbiology (01.04.2024)
Published in Nature reviews. Microbiology (01.04.2024)
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Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy
Thomas, Andrew Maltez, Fidelle, Marine, Routy, Bertrand, Kroemer, Guido, Wargo, Jennifer A., Segata, Nicola, Zitvogel, Laurence
Published in Nature reviews. Clinical oncology (01.09.2023)
Published in Nature reviews. Clinical oncology (01.09.2023)
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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, Segata, Nicola
Published in Nature biotechnology (01.11.2023)
Published in Nature biotechnology (01.11.2023)
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