Zolfo, Moreno
Zolfo, Moreno
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
2020-01-01 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
Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data
2022-01-01 Ciciani, Matteo; Demozzi, Michele; Pedrazzoli, Eleonora; Visentin, Elisabetta; Pezzè, Laura; Signorini, Lorenzo Federico; Blanco-Miguez, Aitor; Zolfo, Moreno; Asnicar, Francesco; Casini, Antonio; Cereseto, Anna; Segata, Nicola
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
2022-01-01 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
Detecting contamination in viromes using ViromeQC
2019-01-01 Zolfo, Moreno; Pinto, Federica; Asnicar, Francesco; Manghi, Paolo; Tett, Adrian; Bushman, Frederic D; Segata, Nicola
Draft genome sequence of the planktic cyanobacterium Tychonema bourrellyi, isolated from Alpine lentic freshwater
2017-01-01 Pinto, Federica; Tett, Adrian; Armanini, Federica; Asnicar, Francesco; Boscaini, Adriano; Pasolli, Edoardo; Zolfo, Moreno; Donati, Claudio; Salmaso, Nico; Segata, Nicola
Draft genome sequences of novel Pseudomonas, Flavobacterium, and Sediminibacterium species strains from a freshwater ecosystem
2018-01-01 Pinto, Federica; Tett, Adrian; Armanini, Federica; Asnicar, Francesco; Boscaini, Adriano; Pasolli, Edoardo; Zolfo, Moreno; Donati, Claudio; Salmaso, Nico; Segata, Nicola
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
2023-01-01 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
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
2019-01-01 Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco; Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice, Benjamin L.; Dulong, Casey; Morgan, Xochitl C.; Golden, Christopher D.; Quince, Christopher; Huttenhower, Curtis; Segata, Nicola
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
2021-01-01 Karcher, N.; Nigro, E.; Puncochar, M.; Blanco-Miguez, A.; Ciciani, M.; Manghi, P.; Zolfo, M.; Cumbo, F.; Manara, S.; Golzato, D.; Cereseto, A.; Arumugam, M.; Bui, T. P. N.; Tytgat, H. L. P.; Valles-Colomer, M.; de Vos, W. M.; Segata, N.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
2021-01-01 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
Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma
2024-01-01 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.
Longitudinal survey of microbiome associated with particulate matter in a megacity
2020-01-01 Qin, Nan; Liang, Peng; Wu, Chunyan; Wang, Guanqun; Xu, Qian; Xiong, Xiao; Wang, Tingting; Zolfo, Moreno; Segata, Nicola; Qin, Huanlong; Knight, Rob; Gilbert, Jack A.; Zhu, Ting F.
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission
2017-01-01 Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Armanini, Federica; Turroni, Francesca; James, Kieran; Ferretti, Pamela; Gorfer, Valentina; Ferrario, Chiara; Milani, Christian; Mangifesta, Marta; Anzalone, Rosaria; Zolfo, Moreno; Viappiani, Alice; Pasolli, Edoardo; Bariletti, Ilaria; Canto, Rosarita; Clementi, Rosanna; Cologna, Marina; Crifò, Tiziana; Cusumano, Giuseppina; Fedi, Sabina; Gottardi, Stefania; Innamorati, Claudia; Masè, Caterina; Postai, Daniela; Savoi, Daniela; Soffiati, Massimo; Tateo, Saverio; Pedrotti, Anna; Segata, Nicola; van Sinderen, Douwe; Ventura, Marco
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
2019-01-01 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
Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
2016-01-01 Ward, Doyle V; Scholz, Matthias Uwe; Zolfo, Moreno; Taft, Diana H.; Schibler, Kurt R.; Tett, Adrian James; Segata, Nicola; Morrow, Ardythe L.
Metagenomics-based discovery of unknown bacteriophages In the human microbiome
2020-10-13 Zolfo, Moreno
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
2017-01-01 Zolfo, Moreno; Tett, Adrian James; Jousson, Olivier; Donati, Claudio; Segata, Nicola
MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice
2023-01-01 Manghi, Paolo; Blanco-Míguez, Aitor; Manara, Serena; Nabinejad, Amir; Cumbo, Fabio; Beghini, Francesco; Armanini, Federica; Golzato, Davide; Huang, Kun D; Thomas, Andrew M; Piccinno, Gianmarco; Punčochář, Michal; Zolfo, Moreno; Lesker, Till R; Bredon, Marius; Planchais, Julien; Glodt, Jeremy; Valles-Colomer, Mireia; Koren, Omry; Pasolli, Edoardo; Asnicar, Francesco; Strowig, Till; Sokol, Harry; Segata, Nicola
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
2019-01-01 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
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
2018-01-01 Ferretti, Pamela; Pasolli, Edoardo; Tett, Adrian; Asnicar, Francesco; Gorfer, Valentina; Fedi, Sabina; Armanini, Federica; Truong, Duy Tin; Manara, Serena; Zolfo, Moreno; Beghini, Francesco; Bertorelli, Roberto; De Sanctis, Veronica; Bariletti, Ilaria; Canto, Rosarita; Clementi, Rosanna; Cologna, Marina; Crifò, Tiziana; Cusumano, Giuseppina; Gottardi, Stefania; Innamorati, Claudia; Masè, Caterina; Postai, Daniela; Savoi, Daniela; Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Turroni, Francesca; Ferrario, Chiara; Milani, Christian; Mangifesta, Marta; Anzalone, Rosaria; Viappiani, Alice; Yassour, Moran; Vlamakis, Hera; Xavier, Ramnik; Collado, Carmen Maria; Koren, Omry; Tateo, Saverio; Soffiati, Massimo; Pedrotti, Anna; Ventura, Marco; Huttenhower, Curtis; Bork, Peer; Segata, Nicola