Asnicar, Francesco

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology

Scientific Computing and Data ManagementGut microbiota and health

Cited by 23,742

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

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 2,303

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,591

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

Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,442

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe

Gut microbiota and healthInfant Nutrition and Health

Cited by 1,292

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,030

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Asnicar, F., Berry, S. E., Valdes, A. M., Nguyen, L. H., Piccinno, G., Drew, D. A., Leeming, E., Gibson, R., Le Roy, C., Khatib, H. A., et al. (2021) · Nature Medicine

Gut microbiota and healthNutrition, Genetics, and Disease

Cited by 995

Human postprandial responses to food and potential for precision nutrition

Berry, S. E., Valdes, A. M., Drew, D. A., Asnicar, F., Mazidi, M., Wolf, J., Capdevila, J., Hadjigeorgiou, G., Davies, R., Al Khatib, H., et al. (2020) · Nature Medicine

Nutrition, Genetics, and DiseaseDiet, Metabolism, and Disease

Cited by 932

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

Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 869

Ketogenic diet and ketone bodies enhance the anticancer effects of PD-1 blockade

Ferrere, G., Tidjani Alou, M., Liu, P., Goubet, A.-G., Fidelle, M., Kepp, O., Durand, S., Iebba, V., Fluckiger, A., Daillère, R., et al. (2021) · JCI Insight

Diet and metabolism studiesCancer Immunotherapy and Biomarkers

Cited by 533

Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver

Bertocchi, A., Carloni, S., Ravenda, P. S., Bertalot, G., Spadoni, I., Lo Cascio, A., Gandini, S., Lizier, M., Braga, D., Asnicar, F., et al. (2021) · Cancer Cell

Cancer Cells and MetastasisGut microbiota and health

Cited by 515

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 476

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine

Cancer Immunotherapy and BiomarkersGut microbiota and health

Cited by 464

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

Yassour, M., Jason, E., Hogstrom, L. J., Arthur, T. D., Tripathi, S., Siljander, H., Selvenius, J., Oikarinen, S., Hyöty, H., Virtanen, S. M., et al. (2018) · Cell Host & Microbe

Gut microbiota and healthInfant Nutrition and Health

Cited by 455

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

Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 449

Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling

Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., et al. (2017) · mSystems

Gut microbiota and healthInfant Nutrition and Health

Cited by 445

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

Ianiro, G., Punčochář, M., Karcher, N., Porcari, S., Armanini, F., Asnicar, F., Beghini, F., Blanco-Míguez, A., Cumbo, F., Manghi, P., et al. (2022) · Nature Medicine

Gut microbiota and healthClostridium difficile and Clostridium perfringens research

Cited by 366

Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma

Björk, J. R., Bolte, L. A., Maltez Thomas, A., Lee, K. A., Rossi, N., Wind, T. T., Smit, L. M., Armanini, F., Asnicar, F., Blanco-Miguez, A., et al. (2024) · Nature Medicine

Gut microbiota and healthCancer Immunotherapy and Biomarkers

Cited by 156

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.

Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 146

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals

Fackelmann, G., Manghi, P., Carlino, N., Heidrich, V., Piccinno, G., Ricci, L., Piperni, E., Arrè, A., Bakker, E., Creedon, A. C., et al. (2025) · Nature Microbiology

Gut microbiota and healthNutritional Studies and Diet

Cited by 142

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., et al. (2020) · Genome Biology

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 116

Detecting contamination in viromes using ViromeQC

Zolfo, M., Pinto, F., Asnicar, F., Manghi, P., Tett, A., Bushman, F. D., & Segata, N. (2019) · Nature Biotechnology

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 103

Immune system and intestinal microbiota determine efficacy of androgen deprivation therapy against prostate cancer

Terrisse, S., Goubet, A.-G., Ueda, K., Thomas, A. M., Quiniou, V., Thelemaque, C., Dunsmore, G., Clave, E., Gamat-Huber, M., Yonekura, S., et al. (2022) · Journal for ImmunoTherapy of Cancer

Prostate Cancer Treatment and ResearchGut microbiota and health

Cited by 80

Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial

Alves Costa Silva, C., Piccinno, G., Suissa, D., Bourgin, M., Schreibelt, G., Durand, S., Birebent, R., Fidelle, M., Sow, C., Aprahamian, F., et al. (2024) · Nature Communications

Gut microbiota and healthCutaneous Melanoma Detection and Management

Cited by 33