Knights, Dan

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 34,887

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

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

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature

Gut microbiota and healthInfant Nutrition and Health

Cited by 7,815

Linking long-term dietary patterns with gut microbial enterotypes

Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science

Gut microbiota and healthNutritional Studies and Diet

Cited by 6,513

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

UniFrac: an effective distance metric for microbial community comparison

Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011) · The ISME Journal

Microbial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Cited by 2,825

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 1,988

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science

Gut microbiota and healthChild Nutrition and Water Access

Cited by 1,173

Moving pictures of the human microbiome

Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 1,138

Enterotypes in the landscape of gut microbial community composition

Costea, P. I., Hildebrand, F., Arumugam, M., Bäckhed, F., Blaser, M. J., Bushman, F. D., de Vos, W. M., Ehrlich, S. D., Fraser, C. M., Hattori, M., et al. (2017) · Nature Microbiology

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 1,138

American Gut: an Open Platform for Citizen-Science Microbiome Research

McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · mSystems

Gut microbiota and healthResearch Data Management Practices

Cited by 878

US immigration westernizes the human gut microbiome

Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 794

Daily sampling reveals personalized diet-microbiome associations in humans

Johnson, A. J., Vangay, P., Al-Ghalith, G. A., Hillmann, B. M., Ward, T. L., Shields-Cutler, R. R., Kim, A. D., Shmagel, A. K., Syed, A. N., Walter, J., et al. (2019) · Cell Host & Microbe

Gut microbiota and healthNutritional Studies and Diet

Cited by 742

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Maldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host & Microbe

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 517

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., & Ley, R. E. (2013) · PLoS Computational Biology

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 508

Evaluating the Information Content of Shallow Shotgun Metagenomics

Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R., & Knights, D. (2018) · mSystems

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 474

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

Knights, D., Lassen, K. G., & Xavier, R. J. (2013) · Gut

Inflammatory Bowel DiseaseGut microbiota and health

Cited by 468

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

Mars, R. A. T., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, H. R., Tang, X., Sun, Z., Kalari, K. R., Korem, T., et al. (2020) · Cell

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 456

Complex host genetics influence the microbiome in inflammatory bowel disease

Knights, D., Silverberg, M. S., Weersma, R. K., Gevers, D., Dijkstra, G., Huang, H., Tyler, A. D., van Sommeren, S., Imhann, F., Stempak, J. M., et al. (2014) · Genome Medicine

Gut microbiota and healthInflammatory Bowel Disease

Cited by 418

Rethinking “Enterotypes”

Knights, D., Ward, T. L., McKinlay, C. E., Miller, H., Gonzalez, A., McDonald, D., & Knight, R. (2014) · Cell Host & Microbe

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 396

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults

Vanegas, S. M., Meydani, M., Barnett, J. B., Goldin, B., Kane, A., Rasmussen, H., Brown, C., Vangay, P., Knights, D., Jonnalagadda, S., et al. (2017) · The American Journal of Clinical Nutrition

Gut microbiota and healthFood composition and properties

Cited by 277

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications

Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology & Therapeutics

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 263

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment

Burns, M. B., Lynch, J., Starr, T. K., Knights, D., & Blekhman, R. (2015) · Genome Medicine

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 231