Franzosa, Eric A.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature

Gut microbiota and healthInflammatory Bowel Disease

Cited by 3,143

Multivariable association discovery in population-scale meta-omics studies

Mallick, H., Rahnavard, A., McIver, L. J., Ma, S., Zhang, Y., Nguyen, L. H., Tickle, T. L., Weingart, G., Ren, B., Schwager, E. H., et al. (2021) · PLOS Computational Biology

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 2,596

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 2,185

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Franzosa, E. A., Sirota-Madi, A., Avila-Pacheco, J., Fornelos, N., Haiser, H. J., Reinker, S., Vatanen, T., Hall, A. B., Mallick, H., McIver, L. J., et al. (2018) · Nature Microbiology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 1,995

Species-level functional profiling of metagenomes and metatranscriptomes

Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 1,693

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

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Vatanen, T., Kostic, A. D., d’Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A.-M., et al. (2016) · Cell

Gut microbiota and healthImmune Response and Inflammation

Cited by 1,289

Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 1,267

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine

Gut microbiota and healthInfant Nutrition and Health

Cited by 1,043

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Paik, D., Yao, L., Zhang, Y., Bae, S., D’Agostino, G. D., Zhang, M., Kim, E., Franzosa, E. A., Avila-Pacheco, J., Bisanz, J. E., et al. (2022) · Nature

Gut microbiota and healthInflammatory Bowel Disease

Cited by 594

Global chemical effects of the microbiome include new bile-acid conjugations

Quinn, R. A., Melnik, A. V., Vrbanac, A., Fu, T., Patras, K. A., Christy, M. P., Bodai, Z., Belda-Ferre, P., Tripathi, A., Chung, L. K., et al. (2020) · Nature

Gut microbiota and healthMetabolomics and Mass Spectrometry Studies

Cited by 579

A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1

Li, W., Hang, S., Fang, Y., Bae, S., Zhang, Y., Zhang, M., Wang, G., McCurry, M. D., Bae, M., Paik, D., et al. (2021) · Cell Host & Microbe

Gut microbiota and healthT-cell and B-cell Immunology

Cited by 306

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque

Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., Miller, A. D., Westmoreland, S. V., Mansfield, K. G., Vallender, E. J., et al. (2015) · Cell Host & Microbe

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 298

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Vatanen, T., Kostic, A. D., d’Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A.-M., et al. (2016) · Cell

Gut microbiota and healthImmune Response and Inflammation

Cited by 298

Experimental design and quantitative analysis of microbial community multiomics

Mallick, H., Ma, S., Franzosa, E. A., Vatanen, T., Morgan, X. C., & Huttenhower, C. (2017) · Genome Biology

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 192

Host genetic variation and its microbiome interactions within the Human Microbiome Project

Kolde, R., Franzosa, E. A., Rahnavard, G., Hall, A. B., Vlamakis, H., Stevens, C., Daly, M. J., Xavier, R. J., & Huttenhower, C. (2018) · Genome Medicine

Gut microbiota and healthGenetic Associations and Epidemiology

Cited by 182

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Ma, S., Shungin, D., Mallick, H., Schirmer, M., Nguyen, L. H., Kolde, R., Franzosa, E., Vlamakis, H., Xavier, R., & Huttenhower, C. (2022) · Genome biology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 164