Francesco Beghini
Francesco Beghini
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Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle
E Pasolli, F Asnicar, S Manara, M Zolfo, N Karcher, F Armanini, F Beghini, ...
Cell 176 (3), 649-662. e20, 2019
Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome
P Ferretti, E Pasolli, A Tett, F Asnicar, V Gorfer, S Fedi, F Armanini, ...
Cell host & microbe 24 (1), 133-145. e5, 2018
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
F Beghini, LJ McIver, A Blanco-Míguez, L Dubois, F Asnicar, S Maharjan, ...
elife 10, e65088, 2021
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
AM Thomas, P Manghi, F Asnicar, E Pasolli, F Armanini, M Zolfo, ...
Nature medicine 25 (4), 667-678, 2019
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
F Asnicar, SE Berry, AM Valdes, LH Nguyen, G Piccinno, DA Drew, ...
Nature medicine 27 (2), 321-332, 2021
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
F Asnicar, AM Thomas, F Beghini, C Mengoni, S Manara, P Manghi, ...
Nature communications 11 (1), 2500, 2020
Accessible, curated metagenomic data through ExperimentHub
E Pasolli, L Schiffer, P Manghi, A Renson, V Obenchain, DT Truong, ...
Nature methods 14 (11), 1023-1024, 2017
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
A Tett, E Pasolli, S Farina, DT Truong, F Asnicar, M Zolfo, F Beghini, ...
npj Biofilms and Microbiomes 3 (1), 14, 2017
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome
F Beghini, E Pasolli, TD Truong, L Putignani, SM Cacciò, N Segata
The ISME journal 11 (12), 2848-2863, 2017
Reporting guidelines for human microbiome research: the STORMS checklist
C Mirzayi, A Renson, Genomic Standards Consortium, ...
Nature medicine 27 (11), 1885-1892, 2021
Critical assessment of metagenome interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver, KN Thompson, M Zolfo, ...
Nature Biotechnology, 1-12, 2023
Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases
G Ianiro, M Punčochář, N Karcher, S Porcari, F Armanini, F Asnicar, ...
Nature Medicine 28 (9), 1913-1923, 2022
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
S Manara, F Asnicar, F Beghini, D Bazzani, F Cumbo, M Zolfo, E Nigro, ...
Genome biology 20 (1), 1-16, 2019
Sociodemographic variation in the oral microbiome
A Renson, HE Jones, F Beghini, N Segata, CP Zolnik, M Usyk, TU Moody, ...
Annals of epidemiology 35, 73-80. e2, 2019
Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study
F Beghini, A Renson, CP Zolnik, L Geistlinger, M Usyk, TU Moody, ...
Annals of epidemiology 34, 18-25. e3, 2019
How inoculation affects the development and the performances of microalgal-bacterial consortia treating real municipal wastewater
S Petrini, P Foladori, F Beghini, F Armanini, N Segata, G Andreottola
Journal of environmental management 263, 110427, 2020
Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines
M Tomasi, M Dalsass, F Beghini, I Zanella, E Caproni, L Fantappiè, ...
Vaccines 9 (11), 1356, 2021
A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples
F Pinto, M Zolfo, F Beghini, F Armanini, F Asnicar, A Silverj, A Boscaini, ...
BioRxiv, 2020.09. 17.302836, 2020
MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice
P Manghi, A Blanco-Míguez, S Manara, A NabiNejad, F Cumbo, F Beghini, ...
Cell Reports 42 (5), 2023
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