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)
Get full text
Journal Article
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)
Get full text
Journal Article
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Wirbel, Jakob, Pyl, Paul Theodor, Kartal, Ece, Zych, Konrad, Kashani, Alireza, Milanese, Alessio, Fleck, Jonas S., Voigt, Anita Y., Palleja, Albert, Ponnudurai, Ruby, Sunagawa, Shinichi, Coelho, Luis Pedro, Schrotz-King, Petra, Vogtmann, Emily, Habermann, Nina, Niméus, Emma, Thomas, Andrew M., Manghi, Paolo, Gandini, Sara, Serrano, Davide, Mizutani, Sayaka, Shiroma, Hirotsugu, Shiba, Satoshi, Shibata, Tatsuhiro, Yachida, Shinichi, Yamada, Takuji, Waldron, Levi, Naccarati, Alessio, Segata, Nicola, Sinha, Rashmi, Ulrich, Cornelia M., Brenner, Hermann, Arumugam, Manimozhiyan, Bork, Peer, Zeller, Georg
Published in Nature medicine (01.04.2019)
Published in Nature medicine (01.04.2019)
Get full text
Journal Article
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)
Get full text
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)
Get full text
Journal Article
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide, Cereseto, Anna, Arumugam, Manimozhiyan, Bui, Thi Phuong Nam, Tytgat, Hanne L P, Valles-Colomer, Mireia, de Vos, Willem M, Segata, Nicola
Published in Genome Biology (14.07.2021)
Published in Genome Biology (14.07.2021)
Get full text
Journal Article
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
Manara, Serena, Asnicar, Francesco, Beghini, Francesco, Bazzani, Davide, Cumbo, Fabio, Zolfo, Moreno, Nigro, Eleonora, Karcher, Nicolai, Manghi, Paolo, Metzger, Marisa Isabell, Pasolli, Edoardo, Segata, Nicola
Published in Genome Biology (28.12.2019)
Published in Genome Biology (28.12.2019)
Get full text
Journal Article
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Karcher, Nicolai, Pasolli, Edoardo, Asnicar, Francesco, Huang, Kun D, Tett, Adrian, Manara, Serena, Armanini, Federica, Bain, Debbie, Duncan, Sylvia H, Louis, Petra, Zolfo, Moreno, Manghi, Paolo, Valles-Colomer, Mireia, Raffaetà, Roberta, Rota-Stabelli, Omar, Collado, Maria Carmen, Zeller, Georg, Falush, Daniel, Maixner, Frank, Walker, Alan W, Huttenhower, Curtis, Segata, Nicola
Published in Genome Biology (08.06.2020)
Published in Genome Biology (08.06.2020)
Get full text
Journal Article
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)
Get full text
Journal Article
Graph-based methods for Author Name Disambiguation: a survey
De Bonis, Michele, Falchi, Fabrizio, Manghi, Paolo
Published in PeerJ. Computer science (11.09.2023)
Published in PeerJ. Computer science (11.09.2023)
Get full text
Journal Article
Profiling microbial strains in urban environments using metagenomic sequencing data
Zolfo, Moreno, Asnicar, Francesco, Manghi, Paolo, Pasolli, Edoardo, Tett, Adrian, Segata, Nicola
Published in Biology direct (09.05.2018)
Published in Biology direct (09.05.2018)
Get full text
Journal Article
Data management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph
Papadopoulou, Elli, Bardi, Alessia, Kakaletris, George, Tziotzios, Diamadis, Manghi, Paolo, Manola, Natalia
Published in Journal of biomedical semantics (02.11.2023)
Published in Journal of biomedical semantics (02.11.2023)
Get full text
Journal Article
We Can Make a Better Use of ORCID: Five Observed Misapplications
Baglioni, Miriam, Manghi, Paolo, Mannocci, Andrea, Bardi, Alessia
Published in Data science journal (31.12.2021)
Published in Data science journal (31.12.2021)
Get full text
Journal Article
Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial
Alves Costa Silva, Carolina, Piccinno, Gianmarco, Suissa, Déborah, Bourgin, Mélanie, Schreibelt, Gerty, Durand, Sylvère, Birebent, Roxanne, Fidelle, Marine, Sow, Cissé, Aprahamian, Fanny, Manghi, Paolo, Punčochář, Michal, Asnicar, Francesco, Pinto, Federica, Armanini, Federica, Terrisse, Safae, Routy, Bertrand, Drubay, Damien, Eggermont, Alexander M. M., Kroemer, Guido, Segata, Nicola, Zitvogel, Laurence, Derosa, Lisa, Bol, Kalijn F., de Vries, I. Jolanda M.
Published in Nature communications (23.02.2024)
Published in Nature communications (23.02.2024)
Get full text
Journal Article
Navigating the unfolding open data landscape in ecology and evolution
Culina, Antica, Baglioni, Miriam, Crowther, Tom W., Visser, Marcel E., Woutersen-Windhouwer, Saskia, Manghi, Paolo
Published in Nature ecology & evolution (01.03.2018)
Published in Nature ecology & evolution (01.03.2018)
Get full text
Journal Article
Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics
Ghensi, Paolo, Manghi, Paolo, Zolfo, Moreno, Armanini, Federica, Pasolli, Edoardo, Bolzan, Mattia, Bertelle, Alberto, Dell’Acqua, Federico, Dellasega, Ester, Waldner, Romina, Tessarolo, Francesco, Tomasi, Cristiano, Segata, Nicola
Published in NPJ biofilms and microbiomes (30.10.2020)
Published in NPJ biofilms and microbiomes (30.10.2020)
Get full text
Journal Article
Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients
Bellerba, Federica, Serrano, Davide, Johansson, Harriet, Pozzi, Chiara, Segata, Nicola, NabiNejad, Amir, Piperni, Elisa, Gnagnarella, Patrizia, Macis, Debora, Aristarco, Valentina, Accornero, Chiara A., Manghi, Paolo, Guerrieri-Gonzaga, Aliana, Biffi, Roberto, Bottiglieri, Luca, Trovato, Cristina, Zampino, Maria Giulia, Corso, Federica, Bellocco, Rino, Raimondi, Sara, Rescigno, Maria, Gandini, Sara
Published in Neoplasia (New York, N.Y.) (01.12.2022)
Published in Neoplasia (New York, N.Y.) (01.12.2022)
Get full text
Journal Article
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
Granehäll, Lena, Huang, Kun D, Tett, Adrian, Manghi, Paolo, Paladin, Alice, O'Sullivan, Niall, Rota-Stabelli, Omar, Segata, Nicola, Zink, Albert, Maixner, Frank
Published in Microbiome (30.09.2021)
Published in Microbiome (30.09.2021)
Get full text
Journal Article
Linking Theory and Practice of Digital Libraries: 26th International Conference on Theory and Practice of Digital Libraries, TPDL 2022, Padua, Italy, September 20-23, 2022, Proceedings
Silvello, Gianmaria, Corcho, Oscar, Manghi, Paolo, Di Nunzio, Giorgio Maria, Golub, Koraljka, Ferro, Nicola, Poggi, Antonella
Year of Publication 2022
Get full text
Year of Publication 2022
eBook