Author

F. Beghini

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 3

Signature Assays, Organisms & Methods

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Assay:metagenomics· 3 Approach:statistical model· 3 Research Focus:benchmarking· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

F. Asnicar· 2 shared M. Zolfo· 2 shared N. Segata· 2 shared A. Blanco-Miguez· 1 shared A. Boscaini· 1 shared A. M. Thomas· 1 shared A. Mailyan· 1 shared A. Silverj· 1 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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2 shared papersMicrobiology

F. Asnicar

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Author profile →

3 papers

Recent·Most cited

Detailed Social Network Interactions and Gut Microbiome Strain-Sharing Within Isolated Honduras Villages

J. Pullman, F. Beghini, M. Alexander, S. Vishnempet Shridhar, D. Prinster, I. L. Brito, N. A. Christakis

The paper investigates how social network interactions influence microbiome composition in isolated Honduran villages using social network and microbiome sequencing data.

Nature · Jan 2, 2025Peer-reviewedMicrobiology

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

F. Beghini, L. J. McIver, A. Blanco-Miguez, L. Dubois, F. Asnicar, S. Maharjan, A. Mailyan, A. M. Thomas, P. Manghi, M. Valles-Colomer, G. Weingart, Y. Zhang, M. Zolfo, C. Huttenhower, E. A. Franzosa, N. Segata

The paper introduces bioBakery 3, a set of tools for microbial community analysis, improving taxonomic, functional, and strain-level profiling with applications to CRC and IBD datasets.

bioRxiv · Nov 19, 2020Microbiology

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, N. Salmaso, N. Segata

The paper evaluates virome enrichment protocols by analyzing microbial community changes during filtration steps in water and sediment samples, finding significant non-viral taxa in the final virome.

bioRxiv · Sep 17, 2020 · PreprintMicrobiology