McDonald, Daniel

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

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

A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature

Microbial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Cited by 2,684

Best practices for analysing microbiomes

Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 2,030

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

Amir, A., McDonald, D., Navas-Molina, J. A., Kopylova, E., Morton, J. T., Zech Xu, Z., Kightley, E. P., Thompson, L. R., Hyde, E. R., Gonzalez, A., et al. (2017) · mSystems

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 1,881

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

Dynamics of the human gut microbiome in inflammatory bowel disease

Halfvarson, J., Brislawn, C. J., Lamendella, R., Vázquez-Baeza, Y., Walters, W. A., Bramer, L. M., D'Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., et al. (2017) · Nature Microbiology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 1,204

GABA-modulating bacteria of the human gut microbiota

Strandwitz, P., Kim, K. H., Terekhova, D., Liu, J. K., Sharma, A., Levering, J., McDonald, D., Dietrich, D., Ramadhar, T. R., Lekbua, A., et al. (2018) · Nature Microbiology

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 1,170

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

He, Y., Wu, W., Zheng, H.-M., Li, P., McDonald, D., Sheng, H.-F., Chen, M.-X., Chen, Z.-H., Ji, G.-Y., Zheng, Z.-D.-X., et al. (2018) · Nature Medicine

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 894

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

Janssen, S., McDonald, D., Gonzalez, A., Navas-Molina, J. A., Jiang, L., Xu, Z. Z., Winker, K., Kado, D. M., Orwoll, E., Manary, M., et al. (2018) · mSystems

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 536

A wellness study of 108 individuals using personal, dense, dynamic data clouds

Price, N. D., Magis, A. T., Earls, J. C., Glusman, G., Levy, R., Lausted, C., McDonald, D. T., Kusebauch, U., Moss, C. L., Zhou, Y., et al. (2017) · Nature Biotechnology

Health, Environment, Cognitive AgingBioinformatics and Genomic Networks

Cited by 427

Extreme Dysbiosis of the Microbiome in Critical Illness

McDonald, D., Ackermann, G., Khailova, L., Baird, C., Heyland, D., Kozar, R., Lemieux, M., Derenski, K., King, J., Vis-Kampen, C., et al. (2016) · mSphere

Gut microbiota and healthSepsis Diagnosis and Treatment

Cited by 426

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

The Microbiome and Human Biology

Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017) · Annual Review of Genomics and Human Genetics

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 373

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects

Nguyen, T. T., Kosciolek, T., Maldonado, Y., Daly, R. E., Martin, A. S., McDonald, D., Knight, R., & Jeste, D. V. (2019) · Schizophrenia Research

Gut microbiota and healthSchizophrenia research and treatment

Cited by 260

Balance Trees Reveal Microbial Niche Differentiation

Morton, J. T., Sanders, J., Quinn, R. A., McDonald, D., Gonzalez, A., Vázquez-Baeza, Y., Navas-Molina, J. A., Song, S. J., Metcalf, J. L., Hyde, E. R., et al. (2017) · mSystems

Microbial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Cited by 254

The impact of skin care products on skin chemistry and microbiome dynamics

Bouslimani, A., da Silva, R., Kosciolek, T., Janssen, S., Callewaert, C., Amir, A., Dorrestein, K., Melnik, A. V., Zaramela, L. S., Kim, J.-N., et al. (2019) · BMC Biology

Dermatology and Skin DiseasesContact Dermatitis and Allergies

Cited by 234

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome

Taylor, B. C., Lejzerowicz, F., Poirel, M., Shaffer, J. P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., et al. (2020) · mSystems

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 203

Effects of the microalgae Chlamydomonas on gastrointestinal health

Fields, F. J., Lejzerowicz, F., Schroeder, D., Ngoi, S. M., Tran, M., McDonald, D., Jiang, L., Chang, J. T., Knight, R., & Mayfield, S. (2020) · Journal of Functional Foods

Gut microbiota and healthSeaweed-derived Bioactive Compounds

Cited by 104

Improving microbial phylogeny with citizen science within a mass-market video game

Sarrazin-Gendron, R., Ghasemloo Gheidari, P., Butyaev, A., Keding, T., Cai, E., Zheng, J., Mutalova, R., Mounthanyvong, J., Zhu, Y., Nazarova, E., et al. (2025) · Nature Biotechnology

Genomics and Phylogenetic StudiesEducational Games and Gamification

Cited by 9