Deliverables
Transcriptomics landscape in dedicated cohorts (GEPAR-TREIZE, PARTNER, PBCP, ONCOBIOTICS, NIRVANA, CHECK’UP)
Immunoscore on most of ONCOBIOME cohorts
Immunoscore on most of ONCOBIOME cohorts using a standardized methodology
Completion of running the metagenomics protocolsCompletion of running the metagenomics protocols on all the samples included in the project
Epidemiological analysisEpidemiological analysis of main flaws in data interpretation
Discovery of commensal-specific regulatory propertiesDiscovery of commensalspecific regulatory properties on immune cell migration
Banking, sequencing and functional description of new commensalsBanking sequencing and functional description of new commensals
Metabolomics on plasmaMetabolomics on plasma in dedicated cohorts
Preliminary dietary dataPreliminary dietary data from existing cohorts where available
Standardization of shotgun microbiome analysisA detailed technical description of standardization of shotgun microbiome analysis on the unified database
Tumor mutational burdenTumor mutational burden and PDL1 for dedicated cohorts
Discovery of commensal-specific metabolitesDiscovery of commensal one or severalspecific metabolites
Freeze of the database of the profilesFreeze of the database of the profiles from all the metagenomes of the project obtained with the tools of D22
Culturomics of E. hiraeCulturomics of E hirae for most cohorts amenable to ICBs
Completion of the curatedCancerMetagenomicData resourcePublications
Author(s):
Francesca Colombo, Oscar Illescas, Sara Noci, Francesca Minnai, Giulia Pintarelli, Angela Pettinicchio, Alberto Vannelli, Luca Sorrentino, Luigi Battaglia, Maurizio Cosimelli, Tommaso A. Dragani & Manuela Gariboldi
Published in:
Scientific Reports, Issue 12, 2022, Page(s) 11424, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-022-15230-6
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Gianluca 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 C
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Nature Medicine, 2022, ISSN 1078-8956
Publisher:
Nature Publishing Group
DOI:
10.1038/s41591-022-01964-3
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Pačínková A., Popovici V.
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BMC Bioinformatics, Issue 23, 2022, Page(s) 351, ISSN 1471-2105
Publisher:
BioMed Central
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10.1186/s12859-022-04891-9
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Nature Medicine, Issue 28, 2022, Page(s) 315-324, ISSN 1078-8956
Publisher:
Nature Publishing Group
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10.1038/s41591-021-01655-5
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Francesco Asnicar; Emily R Leeming; Eirini Dimidi; Mohsen Mazidi; Paul W. Franks; Haya Al Khatib; Ana M. Valdes; Richard Davies; Elco Bakker; Lucy Francis; Andrew T. Chan; Rachel J. Gibson; George Hadjigeorgiou; Jonathan Wolf; Tim D. Spector; Nicola Segata; Sarah Berry
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Gut, Issue 7, 2021, ISSN 0017-5749
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BMJ Publishing Group
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10.1136/gutjnl-2020-323877
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Frontiers in pharmacology., 2021, ISSN 1663-9812
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Frontiers Media S.A.
DOI:
10.3389/fphar.2020.619200
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Francesco Beghini; Lauren J. McIver; Aitor Blanco-Míguez; Leonard Dubois; Francesco Asnicar; Sagun Maharjan; Sagun Maharjan; Ana Mailyan; Ana Mailyan; Paolo Manghi; Matthias Scholz; Andrew Maltez Thomas; Mireia Valles-Colomer; George Weingart; George Weingart; Yancong Zhang; Yancong Zhang; Moreno Zolfo; Curtis Huttenhower; Curtis Huttenhower; Eric A. Franzosa; Eric A. Franzosa; Nicola Segata; Nic
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eLife, Issue 2, 2021, ISSN 2050-084X
Publisher:
eLife Sciences Publications
DOI:
10.7554/elife.65088
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Francesco Asnicar, Sarah E. Berry, Ana M. Valdes, Long H. Nguyen, Gianmarco Piccinno, David A. Drew, Emily Leeming, Rachel Gibson, Caroline 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
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Nature Medicine, 2021, ISSN 1078-8956
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Nature Publishing Group
DOI:
10.1038/s41591-020-01183-8
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Amedeo Gagliardi, Giulia Francescato, Giulio Ferrero, Giovanni Birolo, Sonia Tarallo, Antonio Francavilla, Giulia Piaggeschi, Carla Di Battista, Gaetano Gallo, Alberto Realis Luc, Carlotta Sacerdote, Giuseppe Matullo, Paolo Vineis, Alessio Naccarati, Barbara Pardini
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Cancer Medicine, Issue 00, 2022, Page(s) 1-15, ISSN 2045-7634
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John Wiley & Sons Ltd
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10.1002/cam4.5375
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Antonio Francavilla; Amedeo Gagliardi; Giulia Piaggeschi; Sonia Tarallo; Francesca Cordero; Ruggero G. Pensa; Alessia Impeduglia; Gian Paolo Caviglia; Davide Giuseppe Ribaldone; Gaetano Gallo; Sara Grioni; Giulio Ferrero; Barbara Pardini; Alessio Naccarati
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Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021), Issue 2, 2021, ISSN 2045-2322
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Nature Publishing Group
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10.1038/s41598-021-00014-1
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Genome Biology, Issue 9, 2020, ISSN 1474-7596
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BioMed Central
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10.1186/s13059-020-02042-y
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Sonia Tarallo; Giulio Ferrero; Francesca De Filippis; Antonio Francavilla; Edoardo Pasolli; Valentina Panero; Francesca Cordero; Nicola Segata; Sara Grioni; Ruggero G. Pensa; Barbara Pardini; Danilo Ercolini; Alessio Naccarati
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Gut, Issue 1, 2021, ISSN 1468-3288
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BMJ
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10.1136/gutjnl-2021-325168
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Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
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Springer Nature
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10.1186/s13059-019-1714-3
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Cell Host & Microbe, Issue 26/5, 2019, Page(s) 666-679.e7, ISSN 1931-3128
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Cell Press
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10.1016/j.chom.2019.08.018
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Andrew Maltez Thomas, Nicola Segata
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BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
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BioMed Central
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10.1186/s12915-019-0667-z
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mSystems, Issue 4/5, 2019, ISSN 2379-5077
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American Society for Microbiology Journals
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10.1128/mSystems.00289-19
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Nature Biotechnology, Issue 37/12, 2019, Page(s) 1408-1412, ISSN 1087-0156
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Nature Publishing Group
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10.1038/s41587-019-0334-5
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Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
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Nature Publishing Group
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10.1038/s41467-020-16366-7
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Genome Biology, Issue 4, 2021, ISSN 1474-7596
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BioMed Central
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10.1186/s13059-021-02427-7
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Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, F
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Nature Biotechnology, 2023, ISSN 1087-0156
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Nature Publishing Group
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Nature Medicine, Issue 28, 2022, Page(s) 535-544, ISSN 1078-8956
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Nature Publishing Group
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10.1038/s41591-022-01695-5
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Nature reviews. Microbiology, 2021, ISSN 1740-1526
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Nature Publishing Group
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Nature Medicine, 2020, ISSN 1078-8956
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Nature Publishing Group
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10.1038/s41591-020-0934-0
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Nutrients, 2021, ISSN 2072-6643
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Multidisciplinary Digital Publishing Institute (MDPI)
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10.3390/nu13072234
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Appl Environ Microbiol., 2021, ISSN 0099-2240
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American Society for Microbiology
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10.1128/aem.00471-21
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Cancer Discovery, Issue 12, 2022, Page(s) 1128-1151, ISSN 2159-8274
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American Association for Cancer Research Inc.
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10.1158/2159-8290.cd-21-0999
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Volume 13, Issue 1, 2021, ISSN 2072-6694
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Multidisciplinary Digital Publishing Institute (MDPI)
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10.3390/cancers13194799
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