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Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma Bjork, Johannes R.; Bolte, Laura A.; Thomas, Andrew Maltez; 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, Veronique; Segata, Nicola; Hospers, Geke A. P.; Weersma, Rinse K. Share Save
MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice Manghi, Paolo; Blanco-Miguez, Aitor; Manara, Serena; NabiNejad, Amir; Cumbo, Fabio; Beghini, Francesco; Armanini, Federica; Golzato, Davide; Huang, Kun D.; Thomas, Andrew M.; Piccinno, Gianmarco; Puncochar, 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 Share Save
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 Blanco-Miguez, 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; Puncochar, 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 Share Save
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Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data Ciciani, Matteo; Demozzi, Michele; Pedrazzoli, Eleonora; Visentin, Elisabetta; Pezze, Laura; Signorini, Lorenzo Federico; Blanco-Miguez, Aitor; Zolfo, Moreno; Asnicar, Francesco; Casini, Antonio; Cereseto, Anna; Segata, Nicola Share Save
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma Lee, Karla A.; Thomas, Andrew Maltez; Bolte, Laura A.; Bjork, 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, Veronique; Hospers, Geke A. P.; Spector, Tim D.; Weersma, Rinse K.; Segata, Nicola Share Save
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly Karcher, Nicolai; Nigro, Eleonora; Puncochar, Michal; Blanco-Miguez, 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 Share Save
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Beghini, Francesco; McIver, Lauren J.; Blanco-Miguez, 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 Share Save
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 Share Save
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; Raffaeta, Roberta; Rota-Stabelli, Omar; Carmen Collado, Maria; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W.; Huttenhower, Curtis; Segata, Nicola Share Save
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 Share Save
Longitudinal survey of microbiome associated with particulate matter in a megacity 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. Share Save
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 Share Save
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Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (vol 25, pg 667, 2019) 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, Joao Carlos; Tett, Adrian; Pardini, Barbara; Rescigno, Maria; Waldron, Levi; Naccarati, Alessio; Segata, Nicola Share Save
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, Joao Carlos; Tett, Adrian; Pardini, Barbara; Rescigno, Maria; Waldron, Levi; Naccarati, Alessio; Segata, Nicola Share Save
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Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission 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; Crifo, Tiziana; Cusumano, Giuseppina; Fedi, Sabina; Gottardi, Stefania; Innamorati, Claudia; Mase, Caterina; Postai, Daniela; Savoi, Daniela; Soffiati, Massimo; Tateo, Saverio; Pedrotti, Anna; Segata, Nicola; van Sinderen, Douwe; Ventura, Marco Share Save
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