Beghini, Francesco
Beghini, Francesco
Accessible, curated metagenomic data through ExperimentHub
2017-01-01 Pasolli, Edoardo; Schiffer, Lucas Michael; Manghi, Paolo; Renson, Audrey; Obenchain, Valerie; Truong, Duy Tin; Beghini, Francesco; Malik, Faizan; Ramos, Marcel; Dowd, Jennifer B; Huttenhower, Curtis; Morgan, Martin; Segata, Nicola; Waldron, Levi
Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines
2021-01-01 Tomasi, Michele; Dalsass, Mattia; Beghini, Francesco; Zanella, Ilaria; Caproni, Elena; Fantappiè, Laura; Gagliardi, Assunta; Irene, Carmela; König, Enrico; Frattini, Luca; Masetti, Giulia; Isaac, Samine Jessica; Armanini, Federica; Cumbo, Fabio; Blanco-Míguez, Aitor; Grandi, Alberto; Segata, Nicola; Grandi, Guido
Critical Assessment of Metagenome Interpretation: the second round of challenges
2022-01-01 Meyer, Fernando; Fritz, Adrian; Deng, Zhi-Luo; Koslicki, David; Lesker, Till Robin; Gurevich, Alexey; Robertson, Gary; Alser, Mohammed; Antipov, Dmitry; Beghini, Francesco; Bertrand, Denis; Brito, Jaqueline J; Brown, C Titus; Buchmann, Jan; Buluç, Aydin; Chen, Bo; Chikhi, Rayan; Clausen, Philip T L C; Cristian, Alexandru; Dabrowski, Piotr Wojciech; Darling, Aaron E; Egan, Rob; Eskin, Eleazar; Georganas, Evangelos; Goltsman, Eugene; Gray, Melissa A; Hansen, Lars Hestbjerg; Hofmeyr, Steven; Huang, Pingqin; Irber, Luiz; Jia, Huijue; Jørgensen, Tue Sparholt; Kieser, Silas D; Klemetsen, Terje; Kola, Axel; Kolmogorov, Mikhail; Korobeynikov, Anton; Kwan, Jason; Lapierre, Nathan; Lemaitre, Claire; Li, Chenhao; Limasset, Antoine; Malcher-Miranda, Fabio; Mangul, Serghei; Marcelino, Vanessa R; Marchet, Camille; Marijon, Pierre; Meleshko, Dmitry; Mende, Daniel R; Milanese, Alessio; Nagarajan, Niranjan; Nissen, Jakob; Nurk, Sergey; Oliker, Leonid; Paoli, Lucas; Peterlongo, Pierre; Piro, Vitor C; Porter, Jacob S; Rasmussen, Simon; Rees, Evan R; Reinert, Knut; Renard, Bernhard; Robertsen, Espen Mikal; Rosen, Gail L; Ruscheweyh, Hans-Joachim; Sarwal, Varuni; Segata, Nicola; Seiler, Enrico; Shi, Lizhen; Sun, Fengzhu; Sunagawa, Shinichi; Sørensen, Søren Johannes; Thomas, Ashleigh; Tong, Chengxuan; Trajkovski, Mirko; Tremblay, Julien; Uritskiy, Gherman; Vicedomini, Riccardo; Wang, Zhengyang; Wang, Ziye; Wang, Zhong; Warren, Andrew; Willassen, Nils Peder; Yelick, Katherine; You, Ronghui; Zeller, Georg; Zhao, Zhengqiao; Zhu, Shanfeng; Zhu, Jie; Garrido-Oter, Ruben; Gastmeier, Petra; Hacquard, Stephane; Häußler, Susanne; Khaledi, Ariane; Maechler, Friederike; Mesny, Fantin; Radutoiu, Simona; Schulze-Lefert, Paul; Smit, Nathiana; Strowig, Till; Bremges, Andreas; Sczyrba, Alexander; Mchardy, Alice Carolyn
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
How Inoculation Affects the Development and the Performances of Microalgal-Bacterial Consortia Treating Real Municipal Wastewater
2020-01-01 Petrini, S.; Foladori, P.; Beghini, F.; Armanini, F.; Segata, N.; Andreottola, G.
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
Integrative computational microbial genomics for large-scale metagenomic analyses
2021-03-30 Beghini, Francesco
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome
2017-01-01 Beghini, Francesco; Pasolli, Edoardo; Truong, Tin Duy; Putignani, Lorenza; Cacciò, Simone M; Segata, Nicola
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
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
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
2021-01-01 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
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
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
2020-01-01 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
Reporting guidelines for human microbiome research: the STORMS checklist
2021-01-01 Mirzayi, Chloe; Renson, Audrey; Zohra, Fatima; Elsafoury, Shaimaa; Geistlinger, Ludwig; Kasselman, Lora J; Eckenrode, Kelly; van de Wijgert, Janneke; Loughman, Amy; Marques, Francine Z; Macintyre, David A; Arumugam, Manimozhiyan; Azhar, Rimsha; Beghini, Francesco; Bergstrom, Kirk; Bhatt, Ami; Bisanz, Jordan E; Braun, Jonathan; Bravo, Hector Corrada; Buck, Gregory A; Bushman, Frederic; Casero, David; Clarke, Gerard; Collado, Maria Carmen; Cotter, Paul D; Cryan, John F; Demmer, Ryan T; Devkota, Suzanne; Elinav, Eran; Escobar, Juan S; Fettweis, Jennifer; Finn, Robert D; Fodor, Anthony A; Forslund, Sofia; Franke, Andre; Furlanello, Cesare; Gilbert, Jack; Grice, Elizabeth; Haibe-Kains, Benjamin; Handley, Scott; Herd, Pamela; Holmes, Susan; Jacobs, Jonathan P; Karstens, Lisa; Knight, Rob; Knights, Dan; Koren, Omry; Kwon, Douglas S; Langille, Morgan; Lindsay, Brianna; Mcgovern, Dermot; Mchardy, Alice C; Mcweeney, Shannon; Mueller, Noel T; Nezi, Luigi; Olm, Matthew; Palm, Noah; Pasolli, Edoardo; Raes, Jeroen; Redinbo, Matthew R; Rühlemann, Malte; Balfour Sartor, R; Schloss, Patrick D; Schriml, Lynn; Segal, Eran; Shardell, Michelle; Sharpton, Thomas; Smirnova, Ekaterina; Sokol, Harry; Sonnenburg, Justin L; Srinivasan, Sujatha; Thingholm, Louise B; Turnbaugh, Peter J; Upadhyay, Vaibhav; Walls, Ramona L; Wilmes, Paul; Yamada, Takuji; Zeller, Georg; Zhang, Mingyu; Zhao, Ni; Zhao, Liping; Bao, Wenjun; Culhane, Aedin; Devanarayan, Viswanath; Dopazo, Joaquin; Fan, Xiaohui; Fischer, Matthias; Jones, Wendell; Kusko, Rebecca; Mason, Christopher E; Mercer, Tim R; Sansone, Susanna-Assunta; Scherer, Andreas; Shi, Leming; Thakkar, Shraddha; Tong, Weida; Wolfinger, Russ; Hunter, Christopher; Segata, Nicola; Huttenhower, Curtis; Dowd, Jennifer B; Jones, Heidi E; Waldron, Levi
Sociodemographic variation in the oral microbiome
2019-01-01 Renson, A.; Jones, H. E.; Beghini, F.; Segata, N.; Zolnik, C. P.; Usyk, M.; Moody, T. U.; Thorpe, L.; Burk, R.; Waldron, L.; Dowd, J. B.
Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome
2023-01-01 Manara, Serena; Beghini, Francesco; Masetti, Giulia; Armanini, Federica; Geat, Davide; Galligioni, Giulia; Segata, Nicola; Farina, Stefania; Cristofolini, Mario
Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study
2019-01-01 Beghini, F.; Renson, A.; Zolnik, C. P.; Geistlinger, L.; Usyk, M.; Moody, T. U.; Thorpe, L.; Dowd, J. B.; Burk, R.; Segata, N.; Jones, H. E.; Waldron, L.
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
2017-01-01 Tett, Adrian James; Pasolli, Edoardo; Farina, Stefania; Truong, Duy Tin; Asnicar, Francesco; Zolfo, Moreno; Beghini, Francesco; Armanini, Federica; Jousson, Olivier; De Sanctis, Veronica; Bertorelli, Roberto; Girolomoni, Giampiero; Cristofolini, Mario; Segata, Nicola