20092020

Research output per year

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Research Output

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Review article
2020

A Guide to Diet-Microbiome Study Design

Johnson, A. J., Zheng, J. J., Kang, J. W., Saboe, A., Knights, D. & Zivkovic, A. M., Jun 12 2020, In : Frontiers in Nutrition. 7, 79.

Research output: Contribution to journalReview article

Open Access
2019
Open Access
6 Scopus citations
2018

Functional Genomics of Host–Microbiome Interactions in Humans

Luca, F., Kupfer, S. S., Knights, D., Khoruts, A. & Blekhman, R., Jan 2018, In : Trends in Genetics. 34, 1, p. 30-40 11 p.

Research output: Contribution to journalReview article

Open Access
21 Scopus citations

SHI7 is a self-learning pipeline for multipurpose short-read DNA quality control

Al-Ghalith, G. A., Hillmann, B., Ang, K., Shields-Cutler, R. & Knights, D., May 1 2018, In : mSystems. 3, 3, e00202-17.

Research output: Contribution to journalReview article

Open Access
17 Scopus citations

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., Feb 1 2018, In : Alimentary Pharmacology and Therapeutics. 47, 3, p. 332-345 14 p.

Research output: Contribution to journalReview article

Open Access
52 Scopus citations

The gut microbiome of nonhuman primates: Lessons in ecology and evolution

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., Knight, R., Leigh, S., Stumpf, R., Wolf, T., Glander, K. E., Cabana, F. & Johnson, T. J., Jun 2018, In : American journal of primatology. 80, 6, e22867.

Research output: Contribution to journalReview article

26 Scopus citations
2017

Infant fungal communities: Current knowledge and research opportunities

Ward, T. L., Knights, D. & Gale, C. A., Feb 13 2017, In : BMC medicine. 15, 1, 30.

Research output: Contribution to journalReview article

Open Access
17 Scopus citations
Open Access
11 Scopus citations
2015

Antibiotics, pediatric dysbiosis, and disease

Vangay, P., Ward, T., Gerber, J. S. & Knights, D., May 13 2015, In : Cell Host and Microbe. 17, 5, p. 553-564 12 p.

Research output: Contribution to journalReview article

187 Scopus citations

Bygiene: The new paradigm of bidirectional hygiene

Al-Ghalith, G. A. & Knights, D., Dec 2015, In : Yale Journal of Biology and Medicine. 88, 4, p. 359-365 7 p.

Research output: Contribution to journalReview article

7 Scopus citations
2014

Multi-omics analysis of inflammatory bowel disease

Huang, H., Vangay, P., McKinlay, C. E. & Knights, D., Dec 1 2014, In : Immunology Letters. 162, 2, p. 62-68 7 p.

Research output: Contribution to journalReview article

21 Scopus citations
2012

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., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R. & 1 others, Gordon, J. I., Jun 14 2012, In : Nature. 486, 7402, p. 222-227 6 p.

Research output: Contribution to journalReview article

3161 Scopus citations
2011

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

Zaneveld, J. R. R., Parfrey, L. W., Van Treuren, W., Lozupone, C., Clemente, J. C., Knights, D., Stombaugh, J., Kuczynski, J. & Knight, R., Oct 1 2011, In : Trends in Microbiology. 19, 10, p. 472-482 11 p.

Research output: Contribution to journalReview article

19 Scopus citations

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W. & 78 others, Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S. G., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., Desantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., Gil, I. S., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methé, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spor, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T. & Glöckner, F. O., May 1 2011, In : Nature biotechnology. 29, 5, p. 415-420 6 p.

Research output: Contribution to journalReview article

317 Scopus citations

Supervised classification of human microbiota

Knights, D., Costello, E. K. & Knight, R., Mar 1 2011, In : FEMS Microbiology Reviews. 35, 2, p. 343-359 17 p.

Research output: Contribution to journalReview article

225 Scopus citations
2010

Direct sequencing of the human microbiome readily reveals community differences

Kuczynski, J., Costello, E. K., Nemergut, D. R., Zaneveld, J., Lauber, C. L., Knights, D., Koren, O., Fierer, N., Kelley, S. T., Ley, R. E., Gordon, J. I. & Knight, R., May 5 2010, In : Genome biology. 11, 5, 210.

Research output: Contribution to journalReview article

113 Scopus citations