Nicola Segata

Scopus Author ID ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 111

Top Venues

Nature

Nature communications

Nature medicine

Nature biotechnology

This page only lists publications with an associated author ORCID identifier.

Publications

Giulia Mencattelli, Marie Henriette Dior Ndione, Andrea Silverj, Moussa Moise Diagne, Valentina Curini, Liana Teodori, Marco Di Domenico, Rassoul Mbaye, Alessandra Leone, Maurilia Marcacci, Alioune Gaye, ElHadji Ndiaye, Diawo Diallo, Massimo Ancora, Barbara Secondini, Valeria Di Lollo, Iolanda Mangone, Andrea Bucciacchio, Andrea Polci, Giovanni Marini, Roberto Rosà, Nicola Segata, Gamou Fall, Cesare Cammà, Federica Monaco, Mawlouth Diallo, Omar Rota-Stabelli, Oumar Faye, Annapaola Rizzoli, Giovanni Savini
Spatial and temporal dynamics of West Nile virus between Africa and Europe. Nature communications 14 (1) (2023)
Marta Selma-Royo, Nicola Segata, Liviana Ricci
Human microbiome cultivation expands with AI. Nature biotechnology (2023)
Aitor Blanco-Míguez, Francesco Beghini, Fabio Cumbo, Lauren J McIver, Kelsey N Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D Huang, Andrew Maltez Thomas, William A Nickols, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E Berry, Timothy D Spector, Eric A Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature biotechnology (2023)
Marine Fidelle, Conrad Rauber, Carolina Alves Costa Silva, Ai-Ling Tian, Imran Lahmar, Anne-Laure Mallard de La Varende, Liwei Zhao, Cassandra Thelemaque, Isabelle Lebhar, Meriem Messaoudene, Eugenie Pizzato, Roxanne Birebent, Maxime Descartes Mbogning Fonkou, Silvia Zoppi, Anna Reni, Cécile Dalban, Marion Leduc, Gladys Ferrere, Sylvère Durand, Pierre Ly, Aymeric Silvin, Kevin Mulder, Charles-Antoine Dutertre, Florent Ginhoux, Satoru Yonekura, Maria Paula Roberti, Maryam Tidjani Alou, Safae Terrisse, Jianzhou Chen, Oliver Kepp, Angela Schippers, Norbert Wagner, Javier Suarez-Gosalvez, Sebastian Kobold, Jean-Eudes Fahrner, Corentin Richard, Jacques Bosq, Leonardo Lordello, Giacomo Vitali, Nathalie Galleron, Benoit Quinquis, Emmanuelle Le Chatelier, Lucas Blanchard, Jean-Philippe Girard, Anne Jarry, Nadine Gervois-Segain, Emmanuelle Godefroy, Nathalie Labarrière, Ronald Koschny, Romain Daillère, Benjamin Besse, Caroline Truntzer, François Ghiringhelli, Nicolas Coatnoan, Vanessa Mhanna, David Klatzmann, Damien Drubay, Laurence Albiges, Andrew Maltez Thomas, Nicola Segata, François-Xavier Danlos, Aurélien Marabelle, Bertrand Routy, Lisa Derosa, Guido Kroemer, Laurence Zitvogel
A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers. Science (New York, N.Y.) 380 (6649) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Population-level impacts of antibiotic usage on the human gut microbiome. Nature communications 14 (1) (2023)
Mireia Valles-Colomer, Cristina Menni, Sarah E E Berry, Ana M Valdes, Timothy D Spector, Nicola Segata
Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nature medicine (2023)
Liviana Ricci, Marta Selma-Royo, Davide Golzato, Amir Nabinejad, Charlotte Servais, Federica Armanini, Francesco Asnicar, Federica Pinto, Sabrina Tamburini, Nicola Segata
Draft genome sequence of a representative strain of the Catenibacterium genus isolated from human feces. Microbiology resource announcements (2023)
Nico Salmaso, Adriano Boscaini, Leonardo Cerasino, Massimo Pindo, Federica Pinto, Nicola Segata, Claudio Donati
Draft genome sequence of the anatoxin-a producing cyanobacterium Tychonema bourrellyi B0820 isolated from the epilimnion of the deep Alpine Lake Garda. Microbiology resource announcements (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Mireia Valles-Colomer, Cristina Menni, Sarah E E Berry, Ana M Valdes, Timothy D Spector, Nicola Segata
Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nature medicine 29 (3) (2023)
Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Population-level impacts of antibiotic usage on the human gut microbiome. Nature communications 14 (1) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Francesco Asnicar, Andrew Maltez Thomas, Andrea Passerini, Levi Waldron, Nicola Segata
Machine learning for microbiologists. Nature reviews. Microbiology (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Serena Manara, Francesco Beghini, Giulia Masetti, Federica Armanini, Davide Geat, Giulia Galligioni, Nicola Segata, Stefania Farina, Mario Cristofolini
Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome. Dermatology and therapy (2023)
Mireia Valles-Colomer, Aitor Blanco-Míguez, Paolo Manghi, Francesco Asnicar, Leonard Dubois, Davide Golzato, Federica Armanini, Fabio Cumbo, Kun D Huang, Serena Manara, Giulia Masetti, Federica Pinto, Elisa Piperni, Michal Punčochář, Liviana Ricci, Moreno Zolfo, Olivia Farrant, Adriana Goncalves, Marta Selma-Royo, Ana G Binetti, Jimmy E Becerra, Bei Han, John Lusingu, John H Amuasi, Loredana Amoroso, Alessia Visconti, Claire M Steves, Mario Falchi, Michele Filosi, Adrian Tett, Anna Last, Qian Xu, Nan Qin, Huanlong Qin, Jürgen May, Daniel Eibach, Maria Valeria Corrias, Mirco Ponzoni, Edoardo Pasolli, Timothy D Spector, Enrico Domenici, Maria Carmen Collado, Nicola Segata
The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614 (7946) (2023)
Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Issac Hecht, Aarthi Ravikrishnan, Rafael S Gonçalves, Eric A Franzosa, Karthik Raman, Vincent Carey, Jennifer Beam Dowd, Heidi E Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nature biotechnology (2023)
Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Population-level impacts of antibiotic usage on the human gut microbiome. Nature communications 14 (1) (2023)
Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Population-level impacts of antibiotic usage on the human gut microbiome. Nature communications 14 (1) (2023)
Mireia Valles-Colomer, Cristina Menni, Sarah E E Berry, Ana M Valdes, Timothy D Spector, Nicola Segata
Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nature medicine 29 (3) (2023)
Kihyun Lee, Sebastien Raguideau, Kimmo Sirén, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Population-level impacts of antibiotic usage on the human gut microbiome. Nature communications 14 (1) (2023)
Qian Xu, Chunyan Wu, Qi Zhu, Renyuan Gao, Jianquan Lu, Mireia Valles-Colomer, Jian Zhu, Fang Yin, Linsheng Huang, Lulu Ding, Xiaohui Zhang, Yonghui Zhang, Xiao Xiong, Miaomiao Bi, Xiang Chen, Yefei Zhu, Lin Liu, Yongqiang Liu, Yongshen Chen, Jian Fan, Yan Sun, Jun Wang, Zhan Cao, Chunsun Fan, S Dusko Ehrlich, Nicola Segata, Nan Qin, Huanlong Qin
Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nature aging 2 (5) (2022)
Matteo Ciciani, Michele Demozzi, Eleonora Pedrazzoli, Elisabetta Visentin, Laura Pezzè, Lorenzo Federico Signorini, Aitor Blanco-Míguez, Moreno Zolfo, Francesco Asnicar, Antonio Casini, Anna Cereseto, Nicola Segata
Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data. Nature communications 13 (1) (2022)
Lisa Derosa, Bertrand Routy, Andrew Maltez Thomas, Valerio Iebba, Gérard Zalcman, Sylvie Friard, Julien Mazieres, Clarisse Audigier-Valette, Denis Moro-Sibilot, François Goldwasser, Carolina Alves Costa Silva, Safae Terrisse, Melodie Bonvalet, Arnaud Scherpereel, Hervé Pegliasco, Corentin Richard, François Ghiringhelli, Arielle Elkrief, Antoine Desilets, Felix Blanc-Durand, Fabio Cumbo, Aitor Blanco-Míguez, Romain Boidot, Sandy Chevrier, Romain Daillère, Guido Kroemer, Laurie Alla, Nicolas Pons, Emmanuelle Le Chatelier, Nathalie Galleron, Hugo Roume, Agathe Dubuisson, Nicole Bouchard, Meriem Messaoudene, Damien Drubay, Eric Deutsch, Fabrice Barlesi, David Planchard, Nicola Segata, Stéphanie Martinez, Laurence Zitvogel, Jean-Charles Soria, Benjamin Besse
Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nature medicine 28 (2) (2022)
Safae Terrisse, Anne-Gaelle Goubet, Kousuke Ueda, Andrew Maltez Thomas, Valentin Quiniou, Cassandra Thelemaque, Garett Dunsmore, Emmanuel Clave, Melissa Gamat-Huber, Satoru Yonekura, Gladys Ferrere, Conrad Rauber, Hang Phuong Pham, Jean-Eudes Fahrner, Eugenie Pizzato, Pierre Ly, Marine Fidelle, Marine Mazzenga, Carolina Alves Costa Silva, Federica Armanini, Federica Pinto, Francesco Asnicar, Romain Daillère, Lisa Derosa, Corentin Richard, Pierre Blanchard, Bertrand Routy, Stéphane Culine, Paule Opolon, Aymeric Silvin, Florent Ginhoux, Antoine Toubert, Nicola Segata, Douglas G McNeel, Karim Fizazi, Guido Kroemer, Laurence Zitvogel
Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer. Journal for immunotherapy of cancer 10 (3) (2022)
Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini, null West Nile Working Group
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy. Viruses 15 (1) (2022)
Luca Bianco, Mirko Moser, Andrea Silverj, Diego Micheletti, Giovanni Lorenzin, Lucia Collini, Mattia Barbareschi, Paolo Lanzafame, Nicola Segata, Massimo Pindo, Pietro Franceschi, Omar Rota-Stabelli, Annapaola Rizzoli, Paolo Fontana, Claudio Donati
On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses 14 (3) (2022)
Qian Xu, Chunyan Wu, Qi Zhu, Renyuan Gao, Jianquan Lu, Mireia Valles-Colomer, Jian Zhu, Fang Yin, Linsheng Huang, Lulu Ding, Xiaohui Zhang, Yonghui Zhang, Xiao Xiong, Miaomiao Bi, Xiang Chen, Yefei Zhu, Lin Liu, Yongqiang Liu, Yongshen Chen, Jian Fan, Yan Sun, Jun Wang, Zhan Cao, Chunsun Fan, S Dusko Ehrlich, Nicola Segata, Nan Qin, Huanlong Qin
Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nature aging 2 (5) (2022)
Simone Bihl, Marcus C de Goffau, Daniel Podlesny, Nicola Segata, Fergus Shanahan, Jens Walter, W Florian Fricke
When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome. Gut microbes 14 (1) (2022)
Giulia I Corsi, Swapnil Tichkule, Anna Rosa Sannella, Paolo Vatta, Francesco Asnicar, Nicola Segata, Aaron R Jex, Cock Van Oosterhout, Simone Mario Cacciò
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum. Molecular ecology (2022)
Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini, null West Nile Working Group
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy. Viruses 15 (1) (2022)
Satoru Yonekura, Safae Terrisse, Carolina Alves Costa Silva, Antoine Lafarge, Valerio Iebba, Gladys Ferrere, Anne-Gaëlle Goubet, Jean-Eudes Fahrner, Imran Lahmar, Kousuke Ueda, Gibrail Mansouri, Eugénie Pizzato, Pierre Ly, Marine Mazzenga, Cassandra Thelemaque, Marine Fidelle, Fanny Jaulin, Jérôme Cartry, Marc Deloger, Marine Aglave, Nathalie M Droin, Paule Opolon, Angélique Puget, Fanny Mann, Michel Neunlist, Anne Bessard, Laetitia Aymeric, Tamara Matysiak-Budnik, Jacques Bosq, Paul Hofman, Connie P M Duong, Sophie Ugolini, Valentin Quiniou, Sylvie Berrard, Bernhard Ryffel, Oliver Kepp, Guido Kroemer, Bertrand Routy, Leonardo Lordello, Mohamed Amine Bani, Nicola Segata, Fjodor Yousef Yengej, Hans Clevers, Jean Yves Scoazec, Edoardo Pasolli, Lisa Derosa, Laurence Zitvogel
Cancer Induces a Stress Ileopathy Depending on β-Adrenergic Receptors and Promoting Dysbiosis that Contributes to Carcinogenesis. Cancer discovery 12 (4) (2022)
Qian Xu, Chunyan Wu, Qi Zhu, Renyuan Gao, Jianquan Lu, Mireia Valles-Colomer, Jian Zhu, Fang Yin, Linsheng Huang, Lulu Ding, Xiaohui Zhang, Yonghui Zhang, Xiao Xiong, Miaomiao Bi, Xiang Chen, Yefei Zhu, Lin Liu, Yongqiang Liu, Yongshen Chen, Jian Fan, Yan Sun, Jun Wang, Zhan Cao, Chunsun Fan, S Dusko Ehrlich, Nicola Segata, Nan Qin, Huanlong Qin
Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nature aging 2 (5) (2022)
Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini, null West Nile Working Group
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy. Viruses 15 (1) (2022)
Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini, null West Nile Working Group
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy. Viruses 15 (1) (2022)
Karla A Lee, Andrew Maltez Thomas, Laura A Bolte, Johannes R Björk, Laura Kist de Ruijter, Federica Armanini, Francesco Asnicar, Aitor Blanco-Míguez, Ruth Board, Neus Calbet-Llopart, Lisa Derosa, Nathalie Dhomen, Kelly Brooks, Mark Harland, Mark Harries, Emily R Leeming, Paul C Lorigan, Paolo Manghi, Richard Marais, Julia Newton-Bishop, Luigi Nezi, Federica Pinto, Miriam Potrony, Susana Puig Sardà, Patricio Serra-Bellver, Heather M Shaw, Sabrina Tamburini, Sara Valpione, Amrita Vijay, Levi Waldron, Laurence Zitvogel, Moreno Zolfo, Elisabeth G E de Vries, Paul Nathan, Rudolf S N Fehrmann, Véronique Bataille, Geke A P Hospers, Timothy D Spector, Rinse K Weersma, Nicola Segata
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nature medicine 28 (3) (2022)
Gianluca G Ianiro, Michal Punčochář, Nicolai Karcher, Serena Porcari, Federica Armanini, Francesco Asnicar, Francesco Beghini, Aitor Blanco-Míguez, Fabio Cumbo, Paolo Manghi, Federica Pinto, Luca Masucci, Gianluca Quaranta, Silvia De Giorgi, Giusi Desirè Sciumè, Stefano Bibbò, Federica Del Chierico, Lorenza Putignani, Maurizio Sanguinetti, Antonio Gasbarrini, Mireia Valles-Colomer, Giovanni Cammarota, Nicola Segata
Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nature medicine 28 (9) (2022)
Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini, null West Nile Working Group
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy. Viruses 15 (1) (2022)
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J Brito, C Titus Brown, Jan P Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T L C Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fábio Malcher Miranda, Serghei Mangul, Vanessa R Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C Piro, Jacob S Porter, Simon Rasmussen, Evan R Rees, Knut Reinert, Bernhard Y Renard, Espen Mikal Robertsen, Gail L Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stéphane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature methods 19 (4) (2022)
Qian Xu, Chunyan Wu, Qi Zhu, Renyuan Gao, Jianquan Lu, Mireia Valles-Colomer, Jian Zhu, Fang Yin, Linsheng Huang, Lulu Ding, Xiaohui Zhang, Yonghui Zhang, Xiao Xiong, Miaomiao Bi, Xiang Chen, Yefei Zhu, Lin Liu, Yongqiang Liu, Yongshen Chen, Jian Fan, Yan Sun, Jun Wang, Zhan Cao, Chunsun Fan, S Dusko Ehrlich, Nicola Segata, Nan Qin, Huanlong Qin
Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nature aging 2 (5) (2022)
Michele Tomasi, Mattia Dalsass, Francesco Beghini, Ilaria Zanella, Elena Caproni, Laura Fantappiè, Assunta Gagliardi, Carmela Irene, Enrico König, Luca Frattini, Giulia Masetti, Samine Jessica Isaac, Federica Armanini, Fabio Cumbo, Aitor Blanco-Míguez, Alberto Grandi, Nicola Segata, Guido Grandi
Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines. Vaccines 9 (11) (2021)
Atara Uzan-Yulzari, Olli Turta, Anna Belogolovski, Oren Ziv, Christina Kunz, Sarah Perschbacher, Hadar Neuman, Edoardo Pasolli, Aia Oz, Hila Ben-Amram, Himanshu Kumar, Helena Ollila, Anne Kaljonen, Erika Isolauri, Seppo Salminen, Hanna Lagström, Nicola Segata, Itai Sharon, Yoram Louzoun, Regina Ensenauer, Samuli Rautava, Omry Koren
Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nature communications 12 (1) (2021)
Anne-Gaëlle Goubet, Richard Wheeler, Aurélie Fluckiger, Bo Qu, Fabien Lemaître, Kristina Iribarren, Laura Mondragón, Maryam Tidjani Alou, Eugénie Pizzato, Sylvère Durand, Lisa Derosa, Fanny Aprahamian, Noélie Bossut, Maryse Moya-Nilges, Diane Derrien, Guo Chen, Marion Leduc, Adrien Joseph, Nicolas Pons, Emmanuelle Le Chatelier, Nicola Segata, Satoru Yonekura, Valerio Iebba, Oliver Kepp, Didier Raoult, Fabrice André, Guido Kroemer, Ivo Gomperts Boneca, Laurence Zitvogel, Romain Daillère
Multifaceted modes of action of the anticancer probiotic Enterococcus hirae. Cell death and differentiation 28 (7) (2021)
Giovanni Bacci, Alice Rossi, Federica Armanini, Lisa Cangioli, Ida De Fino, Nicola Segata, Alessio Mengoni, Alessandra Bragonzi, Annamaria Bevivino
Lung and Gut Microbiota Changes Associated with Pseudomonas aeruginosa Infection in Mouse Models of Cystic Fibrosis. International journal of molecular sciences 22 (22) (2021)
Chloe Mirzayi, Audrey Renson, null null, null null, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J Kasselman, Kelly Eckenrode, Janneke van de Wijgert, Amy Loughman, Francine Z Marques, David A MacIntyre, Manimozhiyan Arumugam, Rimsha Azhar, Francesco Beghini, Kirk Bergstrom, Ami Bhatt, Jordan E Bisanz, Jonathan Braun, Hector Corrada Bravo, Gregory A Buck, Frederic Bushman, David Casero, Gerard Clarke, Maria Carmen Collado, Paul D Cotter, John F Cryan, Ryan T Demmer, Suzanne Devkota, Eran Elinav, Juan S Escobar, Jennifer Fettweis, Robert D Finn, Anthony A Fodor, Sofia Forslund, Andre Franke, Cesare Furlanello, Jack Gilbert, Elizabeth Grice, Benjamin Haibe-Kains, Scott Handley, Pamela Herd, Susan Holmes, Jonathan P Jacobs, Lisa Karstens, Rob Knight, Dan Knights, Omry Koren, Douglas S Kwon, Morgan Langille, Brianna Lindsay, Dermot McGovern, Alice C McHardy, Shannon McWeeney, Noel T Mueller, Luigi Nezi, Matthew Olm, Noah Palm, Edoardo Pasolli, Jeroen Raes, Matthew R Redinbo, Malte Rühlemann, R Balfour Sartor, Patrick D Schloss, Lynn Schriml, Eran Segal, Michelle Shardell, Thomas Sharpton, Ekaterina Smirnova, Harry Sokol, Justin L Sonnenburg, Sujatha Srinivasan, Louise B Thingholm, Peter J Turnbaugh, Vaibhav Upadhyay, Ramona L Walls, Paul Wilmes, Takuji Yamada, Georg Zeller, Mingyu Zhang, Ni Zhao, Liping Zhao, Wenjun Bao, Aedin Culhane, Viswanath Devanarayan, Joaquin Dopazo, Xiaohui Fan, Matthias Fischer, Wendell Jones, Rebecca Kusko, Christopher E Mason, Tim R Mercer, Susanna-Assunta Sansone, Andreas Scherer, Leming Shi, Shraddha Thakkar, Weida Tong, Russ Wolfinger, Christopher Hunter, Nicola Segata, Curtis Huttenhower, Jennifer B Dowd, Heidi E Jones, Levi Waldron
Reporting guidelines for human microbiome research: the STORMS checklist. Nature medicine 27 (11) (2021)
Francesco Asnicar, Sarah E Berry, Ana M Valdes, Long H Nguyen, Gianmarco Piccinno, David A Drew, Emily Leeming, Rachel Gibson, Caroline Ivanne Le Roy, Haya Al Khatib, Lucy Francis, Mohsen Mazidi, Olatz Mompeo, Mireia Valles-Colomer, Adrian Tett, Francesco Beghini, Léonard Dubois, Davide Bazzani, Andrew Maltez Thomas, Chloe Mirzayi, Asya Khleborodova, Sehyun Oh, Rachel Hine, Christopher Bonnett, Joan Capdevila Pujol, Serge Danzanvilliers, Francesca Giordano, Ludwig Geistlinger, Levi Waldron, Richard Davies, George Hadjigeorgiou, Jonathan Wolf, José Marìa Ordovàs, Christopher D Gardner, Paul W Franks, Andrew T Chan, Curtis Huttenhower, Timothy D Spector, Nicola Segata
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature medicine 27 (2) (2021)
Mireia Valles-Colomer, Rodrigo Bacigalupe, Sara Vieira-Silva, Shinya Suzuki, Youssef Darzi, Raul Yhossef Tito Tadeo, Takuji Yamada, Nicola Segata, Jeroen Raes, Gwen Falony
Variation and transmission of the human gut microbiota across multiple familial generations. Nature microbiology 7 (1) (2021)
Marsha C Wibowo, Zhen Yang, Maxime Borry, Alexander Hübner, Kun D Huang, Braden T Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto Garcia-Ortiz, Angélica Martínez-Hernández, Jacob M Luber, Philipp Kirstahler, Tre Blohm, Francis E Smiley, Richard Arnold, Sonia A Ballal, Sünje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco-Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar David Kostic
Reconstruction of ancient microbial genomes from the human gut. Nature 594 (7862) (2021)
Sonia Tarallo, Giulio Ferrero, Francesca De Filippis, Antonio Francavilla, Edoardo Pasolli, Valentina Panero, Francesca Cordero, Nicola Segata, Sara Grioni, Ruggero Gaetano Pensa, Barbara Pardini, Danilo Ercolini, Alessio Naccarati
Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals. Gut (2021)
Buck T Hanson, K Dimitri Kits, Jessica Löffler, Anna G Burrichter, Alexander Fiedler, Karin Denger, Benjamin Frommeyer, Craig W Herbold, Thomas Rattei, Nicolai Karcher, Nicola Segata, David Schleheck, Alexander Loy
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. The ISME journal 15 (9) (2021)
Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L P Tytgat, Mireia Valles-Colomer, Willem M de Vos, Nicola Segata
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome biology 22 (1) (2021)
Safae Terrisse, Lisa Derosa, Valerio Iebba, François Ghiringhelli, Ines Vaz-Luis, Guido Kroemer, Marine Fidelle, Stergios Christodoulidis, Nicola Segata, Andrew Maltez Thomas, Anne-Laure Martin, Aude Sirven, Sibille Everhard, Fanny Aprahamian, Nitharsshini Nirmalathasan, Romy Aarnoutse, Marjolein Smidt, Janine Ziemons, Carlos Caldas, Sibylle Loibl, Carsten Denkert, Sylvere Durand, Claudia Iglesias, Filippo Pietrantonio, Bertrand Routy, Fabrice André, Edoardo Pasolli, Suzette Delaloge, Laurence Zitvogel
Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. Cell death and differentiation 28 (9) (2021)
Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10 (2021)
Adrian Tett, Edoardo Pasolli, Giulia Masetti, Danilo Ercolini, Nicola Segata
Prevotella diversity, niches and interactions with the human host. Nature reviews. Microbiology 19 (9) (2021)
Davide Serrano, Chiara Pozzi, Silvia Guglietta, Bruno Fosso, Mariano Suppa, Patrizia Gnagnarella, Federica Corso, Federica Bellerba, Debora Macis, Valentina Aristarco, Paolo Manghi, Nicola Segata, Cristina Trovato, Maria Giulia Zampino, Marinella Marzano, Bernardo Bonanni, Maria Rescigno, Sara Gandini
Microbiome as Mediator of Diet on Colorectal Cancer Risk: The Role of Vitamin D, Markers of Inflammation and Adipokines. Nutrients 13 (2) (2021)
Edoardo Pasolli, Francesca De Filippis, Italia E Mauriello, Fabio Cumbo, Aaron M Walsh, John Leech, Paul D Cotter, Nicola Segata, Danilo Ercolini
Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature communications 11 (1) (2020)
David Wylensek, Thomas C A Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R Lesker, Sara B Hernández, Viktoria Heine, Eva M Buhl, Paul M D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R Parreira, Birte Abt, Heidi L Doden, Lindsey Ly, João M P Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J Taverne-Thiele, Marcel Giesbers, Jerry M Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M Ridlon, Tobias A M Gulder, Joerg Overmann, Thomas Clavel
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature communications 11 (1) (2020)
Elena Zagato, Chiara Pozzi, Alice Bertocchi, Tiziana Schioppa, Fabiana Saccheri, Silvia Guglietta, Bruno Fosso, Laura Melocchi, Giulia Nizzoli, Jacopo Troisi, Marinella Marzano, Bianca Oresta, Ilaria Spadoni, Koji Atarashi, Sara Carloni, Stefania Arioli, Giulia Fornasa, Francesco Asnicar, Nicola Segata, Simone Guglielmetti, Kenya Honda, Graziano Pesole, William Vermi, Giuseppe Penna, Maria Rescigno
Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth. Nature microbiology 5 (3) (2020)
Aurélie Fluckiger, Romain Daillère, Mohamed Sassi, Barbara Susanne Sixt, Peng Liu, Friedemann Loos, Corentin Richard, Catherine Rabu, Maryam Tidjani Alou, Anne-Gaëlle Goubet, Fabien Lemaitre, Gladys Ferrere, Lisa Derosa, Connie P M Duong, Meriem Messaoudene, Andréanne Gagné, Philippe Joubert, Luisa De Sordi, Laurent Debarbieux, Sylvain Simon, Clara-Maria Scarlata, Maha Ayyoub, Belinda Palermo, Francesco Facciolo, Romain Boidot, Richard Wheeler, Ivo Gomperts Boneca, Zsófia M Sztupinszki, Krisztian Papp, Istvan Csabai, Edoardo Pasolli, Nicola Segata, Carlos López-Otín, Zoltan Szallasi, Fabrice Andre, Valerio Iebba, Valentin Quiniou, David Klatzmann, Jacques Boukhalil, Saber Khelaifia, Didier Raoult, Laurence Albiges, Bernard Escudier, Alexander Eggermont, Fathia Mami-Chouaib, Paola Nistico, François Ghiringhelli, Bertrand Routy, Nathalie Labarrière, Vincent Cattoir, Guido Kroemer, Laurence Zitvogel
Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science (New York, N.Y.) 369 (6506) (2020)
Maria Carmen Collado, Nicola Segata
Initial exploration of in utero microbial colonization. Nature medicine 26 (4) (2020)
Giacomo Caio, Lisa Lungaro, Nicola Segata, Matteo Guarino, Giorgio Zoli, Umberto Volta, Roberto De Giorgio
Effect of Gluten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity. Nutrients 12 (6) (2020)
Sonia Tarallo, Giulio Ferrero, Gaetano Gallo, Antonio Francavilla, Giuseppe Clerico, Alberto Realis Luc, Paolo Manghi, Andrew Maltez Thomas, Paolo Vineis, Nicola Segata, Barbara Pardini, Alessio Naccarati, Francesca Cordero
Correction for Tarallo et al., "Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples". mSystems 5 (1) (2020)
Gianluca G Ianiro, Ernesto Rossi, Andrew Maltez Thomas, Giovanni Schinzari, Luca Masucci, Gianluca Quaranta, Carlo Romano Settanni, Loris Riccardo Lopetuso, Federica Armanini, Aitor Blanco-Miguez, Francesco Asnicar, Clarissa Consolandi, Roberto Iacovelli, Maurizio Sanguinetti, Giampaolo Tortora, Antonio Gasbarrini, Nicola Segata, Giovanni Cammarota
Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma. Nature communications 11 (1) (2020)
Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun D Huang, Adrian Tett, Serena Manara, Federica Armanini, Debbie Bain, Sylvia H Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Valles-Colomer, Roberta Raffaetà, Omar Rota-Stabelli, Maria Carmen Collado, Georg Zeller, Daniel Falush, Frank Maixner, Alan W Walker, Curtis Huttenhower, Nicola Segata
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome biology 21 (1) (2020)
Moreno Zolfo, Federica Pinto, Francesco Asnicar, Paolo Manghi, Adrian Tett, Frederic D Bushman, Nicola Segata
Detecting contamination in viromes using ViromeQC. Nature biotechnology 37 (12) (2020)
Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martin Beracochea, Zhou Jason Shi, Katherine S Pollard, Ekaterina Sakharova, Donovan H Parks, Philip Hugenholtz, Nicola Segata, Nikos C Kyrpides, Robert D Finn
A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature biotechnology 39 (1) (2020)
Giovanni Bacci, Giovanni Taccetti, Daniela Dolce, Federica Armanini, Nicola Segata, Francesca Di Cesare, Vincenzina Lucidi, Ersilia Fiscarelli, Patrizia Morelli, Rosaria Casciaro, Anna Negroni, Alessio Mengoni, Annamaria Bevivino
Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms 8 (7) (2020)
Paolo Ghensi, Paolo Manghi, Moreno Zolfo, Federica Armanini, Edoardo Pasolli, Mattia Bolzan, Alberto Bertelle, Federico Dell'Acqua, Ester Dellasega, Romina Waldner, Francesco Tessarolo, Cristiano Tomasi, Nicola Segata
Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics. NPJ biofilms and microbiomes 6 (1) (2020)
Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, Nicola Segata
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature communications 11 (1) (2020)
Thomas Yssing Michaelsen, Jakob Brandt, Caitlin Margaret Singleton, Rasmus Hansen Kirkegaard, Johanna Wiesinger, Nicola Segata, Mads Albertsen
The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities. mSystems 5 (1) (2020)
Sarah E Berry, Ana M Valdes, David A Drew, Francesco Asnicar, Mohsen Mazidi, Jonathan Wolf, Joan Capdevila Pujol, George Hadjigeorgiou, Richard Davies, Haya Al Khatib, Christopher Bonnett, Sajaysurya Ganesh, Elco Bakker, Deborah J Hart, Massimo Mangino, Ruth J F Loos, Inbar Linenberg, Patrick Wyatt, José Marìa Ordovàs, Christopher D Gardner, Linda M Delahanty, Andrew T Chan, Nicola Segata, Paul W Franks, Timothy D Spector
Human postprandial responses to food and potential for precision nutrition. Nature medicine 26 (6) (2020)
Matthias Scholz, Davide Albanese, Kieran Michael Tuohy, Claudio Donati, Nicola Segata, Omar Rota-Stabelli
Large scale genome reconstructions illuminate Wolbachia evolution. Nature communications 11 (1) (2020)
Laura Selbmann, Zsigmond Benkő, Claudia Coleine, Gerrit Sybren de Hoog, Claudio Donati, Irina Druzhinina, Tamás Emri, Cassandra L Ettinger, Amy S Gladfelter, Anna A Gorbushina, Igor V Grigoriev, Martin Grube, Nina Gunde Cimerman, Zsolt Ákos Karányi, Beatrix Kocsis, Tania Kubressoian, Ida Miklós, Márton Miskei, Lucia Muggia, Trent R Northen, Monika Novak Babič, Christa Pennacchio, Walter P Pfliegler, Istvàn Pòcsi, Valeria Prigione, Meritxell Riquelme, Nicola Segata, Julia Schumacher, Ekaterina Shelest, Katja Sterflinger, Donatella Tesei, Jana M U Ren, Giovanna Cristina Varese, Xabier Vázquez-Campos, Vania A Vicente, Emanuel Maltempi de Souza, Polona Zalar, Allison K Walker, Jason E Stajich
Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES. Life (Basel, Switzerland) 10 (12) (2020)
Serena Manara, Francesco Asnicar, Francesco Beghini, Davide Bazzani, Fabio Cumbo, Moreno Zolfo, Eleonora Nigro, Nicolai Karcher, Paolo Manghi, Marisa Isabell Metzger, Edoardo Pasolli, Nicola Segata
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome biology 20 (1) (2019)
Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron
Accessible, curated metagenomic data through ExperimentHub. Nature methods 14 (11) (2019)
Sander Wuyts, Nicola Segata
At the forefront of the sequencing revolution-notes from the RNGS19 conference. Genome biology 20 (1) (2019)
Daniela Dolce, Stella Neri, Laura Grisotto, Silvia Campana, Novella Ravenni, Francesca Miselli, Erica Camera, Lucia Zavataro, Cesare Braggion, Ersilia V Fiscarelli, Vincenzina Lucidi, Lisa Cariani, Daniela Girelli, Nadia Faelli, Carla Colombo, Cristina Lucanto, Mariangela Lombardo, Giuseppe Magazzù, Antonella Tosco, Valeria Raia, Serena Manara, Edoardo Pasolli, Federica Armanini, Nicola Segata, Annibale Biggeri, Giovanni Taccetti
Methicillin-resistant Staphylococcus aureus eradication in cystic fibrosis patients: A randomized multicenter study. PloS one 14 (3) (2019)
Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G Sanders, Pedro Belda-Ferre, Gabriel A Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B Yin, Shi Huang, Nimaichand Salam, Jian-Yu Jiao, Zijun Wu, Zhenjiang Z Xu, Kalen Cantrell, Yimeng Yang, Erfan Sayyari, Maryam Rabiee, James T Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature communications 10 (1) (2019)
Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Niméus, Andrew Maltez Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature medicine 25 (4) (2019)
Sonia Tarallo, Giulio Ferrero, Gaetano Gallo, Antonio Francavilla, Giuseppe Clerico, Alberto Realis Luc, Paolo Manghi, Andrew Maltez Thomas, Paolo Vineis, Nicola Segata, Barbara Pardini, Alessio Naccarati, Francesca Cordero
Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. mSystems 4 (5) (2019)
Andrew Maltez Thomas, Nicola Segata
Multiple levels of the unknown in microbiome research. BMC biology 17 (1) (2019)
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric John Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodriguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan P Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo-Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine A Lozupone, Massoud Maher, Clarisse A Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima R Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam R Rivers, Michael Scott Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin Johan Jozias van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37 (8) (2019)
Andrew J McBain, Catherine A O'Neill, Alejandro Amezquita, Laura J Price, Karoline Faust, Adrian Tett, Nicola Segata, Jonathan R Swann, Adrian M Smith, Barry Murphy, Michael Hoptroff, Gordon James, Yugandhar Reddy, Anindya Dasgupta, Tom Ross, Iain L Chapple, William G Wade, Judith Fernandez-Piquer
Consumer Safety Considerations of Skin and Oral Microbiome Perturbation. Clinical microbiology reviews 32 (4) (2019)
Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, Edoardo Pasolli, Federica Armanini, Moreno Zolfo, Francesco Beghini, Serena Manara, Nicolai Karcher, Chiara Pozzi, Sara Gandini, Davide Serrano, Sonia Tarallo, Antonio Francavilla, Gaetano Gallo, Mario Trompetto, Giulio Ferrero, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Jakob Wirbel, Petra Schrotz-King, Cornelia M Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller, Francesca Cordero, Emmanuel Dias-Neto, João Carlos Setubal, Adrian Tett, Barbara Pardini, Maria Rescigno, Levi Waldron, Alessio Naccarati, Nicola Segata
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature medicine 25 (4) (2019)
Serena Manara, Edoardo Pasolli, Daniela Dolce, Novella Ravenni, Silvia Campana, Federica Armanini, Francesco Asnicar, Alessio Mengoni, Luisa Galli, Carlotta Montagnani, Elisabetta Venturini, Omar Rota-Stabelli, Guido Grandi, Giovanni Taccetti, Nicola Segata
Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome medicine 10 (1) (2018)
Federica Pinto, Adrian Tett, Federica Armanini, Francesco Asnicar, Adriano Boscaini, Edoardo Pasolli, Moreno Zolfo, Claudio Donati, Nico Salmaso, Nicola Segata
Correction for Pinto et al., "Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Strains from a Freshwater Ecosystem". Genome announcements 6 (10) (2018)
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
Profiling microbial strains in urban environments using metagenomic sequencing data. Biology direct 13 (1) (2018)
Eric A Franzosa, Lauren J McIver, Gholamali Rahnavard, Luke R Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, J Gregory Caporaso, Nicola Segata, Curtis Huttenhower
Species-level functional profiling of metagenomes and metatranscriptomes. Nature methods 15 (11) (2018)
Nicola Segata
On the Road to Strain-Resolved Comparative Metagenomics. mSystems 3 (2) (2018)
Angelo Joshua Victoria, Ernelea Cao, Nico Salmaso, Nicola Segata, Claudio Donati
Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria. Microbiology resource announcements 7 (8) (2018)

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Nicola Segata