Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

por Chicco, Davide, Cumbo, Fabio, Angione, Claudio
Publicado 2023

Investigating transcription factor synergism in humans

por Cumbo, Fabio, Vergni, Davide, Santoni, Daniele
Publicado 2018

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas

por Cumbo, Fabio, Fiscon, Giulia, Ceri, Stefano, Masseroli, Marco, Weitschek, Emanuel
Publicado 2017

GIANT: A Cytoscape Plugin for Modular Networks

por Cumbo, Fabio, Paci, Paola, Santoni, Daniele, Di Paola, Luisa, Giuliani, Alessandro
Publicado 2014

Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks

por Apollonio, Nicola, Blankenberg, Daniel, Cumbo, Fabio, Franciosa, Paolo Giulio, Santoni, Daniele
Publicado 2022

Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer’s disease like pathology

por Arisi, Ivan, D’Onofrio, Mara, Brandi, Rossella, Cattaneo, Antonino, Bertolazzi, Paola, Cumbo, Fabio, Felici, Giovanni, Guerra, Concettina
Publicado 2015

Population-level impacts of antibiotic usage on the human gut microbiome

por Lee, Kihyun, Raguideau, Sebastien, Sirén, Kimmo, Asnicar, Francesco, Cumbo, Fabio, Hildebrand, Falk, Segata, Nicola, Cha, Chang-Jun, Quince, Christopher
Publicado 2023

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

por Pasolli, Edoardo, De Filippis, Francesca, Mauriello, Italia E., Cumbo, Fabio, Walsh, Aaron M., Leech, John, Cotter, Paul D., Segata, Nicola, Ercolini, Danilo
Publicado 2020

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

por 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
Publicado 2019

An ontology-based approach for modelling and querying Alzheimer’s disease data

por Taglino, Francesco, Cumbo, Fabio, Antognoli, Giulia, Arisi, Ivan, D’Onofrio, Mara, Perazzoni, Federico, Voyat, Roger, Fiscon, Giulia, Conte, Federica, Canevelli, Marco, Bruno, Giuseppe, Mecocci, Patrizia, Bertolazzi, Paola
Publicado 2023

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

por 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
Publicado 2020

Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines

por 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
Publicado 2021

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

por 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
Publicado 2021

Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population

por Manara, Serena, Selma-Royo, Marta, Huang, Kun D., Asnicar, Francesco, Armanini, Federica, Blanco-Miguez, Aitor, Cumbo, Fabio, Golzato, Davide, Manghi, Paolo, Pinto, Federica, Valles-Colomer, Mireia, Amoroso, Loredana, Corrias, Maria Valeria, Ponzoni, Mirco, Raffaetà, Roberta, Cabrera-Rubio, Raul, Olcina, Mari, Pasolli, Edoardo, Collado, Maria Carmen, Segata, Nicola
Publicado 2023

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

por Ianiro, Gianluca, Punčochář, Michal, Karcher, Nicolai, Porcari, Serena, Armanini, Federica, Asnicar, Francesco, Beghini, Francesco, Blanco-Míguez, Aitor, Cumbo, Fabio, Manghi, Paolo, Pinto, Federica, Masucci, Luca, Quaranta, Gianluca, De Giorgi, Silvia, Sciumè, Giusi Desirè, Bibbò, Stefano, Del Chierico, Federica, Putignani, Lorenza, Sanguinetti, Maurizio, Gasbarrini, Antonio, Valles-Colomer, Mireia, Cammarota, Giovanni, Segata, Nicola
Publicado 2022

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

por 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
Publicado 2023

Outer Membrane Vesicles From The Gut Microbiome Contribute to Tumor Immunity by Eliciting Cross-Reactive T Cells

por Tomasi, Michele, Caproni, Elena, Benedet, Mattia, Zanella, Ilaria, Giorgetta, Sebastiano, Dalsass, Mattia, König, Enrico, Gagliardi, Assunta, Fantappiè, Laura, Berti, Alvise, Tamburini, Silvia, Croia, Lorenzo, Di Lascio, Gabriele, Bellini, Erika, Valensin, Silvia, Licata, Giada, Sebastiani, Guido, Dotta, Francesco, Armanini, Federica, Cumbo, Fabio, Asnicar, Francesco, Blanco-Míguez, Aitor, Ruggiero, Eliana, Segata, Nicola, Grandi, Guido, Grandi, Alberto
Publicado 2022

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

por 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
Publicado 2023

The person-to-person transmission landscape of the gut and oral microbiomes

por Valles-Colomer, Mireia, Blanco-Míguez, Aitor, Manghi, Paolo, Asnicar, Francesco, Dubois, Leonard, Golzato, Davide, Armanini, Federica, Cumbo, Fabio, Huang, Kun D., Manara, Serena, Masetti, Giulia, Pinto, Federica, Piperni, Elisa, Punčochář, Michal, Ricci, Liviana, Zolfo, Moreno, Farrant, Olivia, Goncalves, Adriana, Selma-Royo, Marta, Binetti, Ana G., Becerra, Jimmy E., Han, Bei, Lusingu, John, Amuasi, John, Amoroso, Loredana, Visconti, Alessia, Steves, Claire M., Falchi, Mario, Filosi, Michele, Tett, Adrian, Last, Anna, Xu, Qian, Qin, Nan, Qin, Huanlong, May, Jürgen, Eibach, Daniel, Corrias, Maria Valeria, Ponzoni, Mirco, Pasolli, Edoardo, Spector, Tim D., Domenici, Enrico, Collado, Maria Carmen, Segata, Nicola
Publicado 2023

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

por Wylensek, David, Hitch, Thomas C. A., Riedel, Thomas, Afrizal, Afrizal, Kumar, Neeraj, Wortmann, Esther, Liu, Tianzhe, Devendran, Saravanan, Lesker, Till R., Hernández, Sara B., Heine, Viktoria, Buhl, Eva M., M. D’Agostino, Paul, Cumbo, Fabio, Fischöder, Thomas, Wyschkon, Marzena, Looft, Torey, Parreira, Valeria R., Abt, Birte, Doden, Heidi L., Ly, Lindsey, Alves, João M. P., Reichlin, Markus, Flisikowski, Krzysztof, Suarez, Laura Navarro, Neumann, Anthony P., Suen, Garret, de Wouters, Tomas, Rohn, Sascha, Lagkouvardos, Ilias, Allen-Vercoe, Emma, Spröer, Cathrin, Bunk, Boyke, Taverne-Thiele, Anja J., Giesbers, Marcel, Wells, Jerry M., Neuhaus, Klaus, Schnieke, Angelika, Cava, Felipe, Segata, Nicola, Elling, Lothar, Strowig, Till, Ridlon, Jason M., Gulder, Tobias A. M., Overmann, Jörg, Clavel, Thomas
Publicado 2020