Huttenhower, Curtis

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

Metagenomic biomarker discovery and explanation

Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 16,192

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 9,116

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe

Gut microbiota and healthInflammatory Bowel Disease

Cited by 3,220

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

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., Reyes, J. A., Shah, S. A., LeLeiko, N., Snapper, S. B., et al. (2012) · Genome Biology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 2,713

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

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife

Gut microbiota and healthRheumatoid Arthritis Research and Therapies

Cited by 2,047

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

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,960

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., et al. (2016) · Science

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,914

The healthy human microbiome

Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 1,891

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Geller, L. T., Barzily-Rokni, M., Danino, T., Jonas, O. H., Shental, N., Nejman, D., Gavert, N., Zwang, Y., Cooper, Z. A., Shee, K., et al. (2017) · Science

Pancreatic and Hepatic Oncology ResearchBacterial Cancer Therapy

Cited by 1,817

Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,776

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

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

Microbial co-occurrence relationships in the human microbiome

Faust, K., Sathirapongsasuti, J. F., Izard, J., Segata, N., Gevers, D., Raes, J., & Huttenhower, C. (2012) · PLoS Computational Biology

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,527

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

The Integrative Human Microbiome Project

The Integrative HMP (iHMP) Research Network Consortium, Proctor, L. M., Creasy, H. H., Fettweis, J. M., Lloyd-Price, J., Mahurkar, A., Zhou, W., Buck, G. A., Snyder, M. P., Strauss, J. F., et al. (2019) · Nature

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,381

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

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