Research Output per year
Research Output 1991 2019
- 1 - 50 out of 98 results
- Publication Year, Title (descending)
Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development
Pearson, T. R., Caporaso, J. G., Yellowhair, M., Bokulich, N. A., Padi, M., Roe, D. J., Wertheim, B. C., Linhart, M., Martinez, J. A., Bilagody, C., Hornstra, H., Alberts, D. S., Lance, P. & Thompson, P. A., Feb 1 2019, In : Cancer Medicine. 8, 2, p. 617-628 12 p.Research output: Contribution to journal › Article
Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota
Kang, D. W., Adams, J. B., Coleman, D. M., Pollard, E. L., Maldonado, J., McDonough-Means, S., Caporaso, J. G. & Krajmalnik-Brown, R., Dec 1 2019, In : Scientific Reports. 9, 1, 5821.Research output: Contribution to journal › Article
Rapidly processed stool swabs approximate stool microbiota profiles
Bokulich, N. A., Maldonado, J., Kang, D. W., Krajmalnik-Brown, R. & Caporaso, J. G., Mar 1 2019, In : mSphere. 4, 2, e00208-19.Research output: Contribution to journal › Article
Species abundance information improves sequence taxonomy classification accuracy
Kaehler, B. D., Bokulich, N. A., McDonald, D., Knight, R., Caporaso, J. G. & Huttley, G. A., Dec 1 2019, In : Nature Communications. 10, 1, 4643.Research output: Contribution to journal › Article
UAV wildlife radiotelemetry: System and methods of localization
Shafer, M. W., Vega, G., Rothfus, K. & Flikkema, P. G., Jan 1 2019, (Accepted/In press) In : Methods in Ecology and Evolution.Research output: Contribution to journal › Article
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., Melnik, A. V., Morton, J. T., Navas, J., Quinn, R. A., Sanders, J. G., Swafford, A. D., Thompson, L. R., Tripathi, A., Xu, Z. Z., Zaneveld, J. R. & 3 others, , May 23 2018, (Accepted/In press) In : Nature Reviews Microbiology. p. 1-13 13 p.Research output: Contribution to journal › Article
Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: Report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018
Meisel, J. S., Nasko, D. J., Brubach, B., Cepeda-Espinoza, V., Chopyk, J., Corrada-Bravo, H., Fedarko, M., Ghurye, J., Javkar, K., Olson, N. D., Shah, N., Allard, S. M., Bazinet, A. L., Bergman, N. H., Brown, A., Caporaso, J. G., Conlan, S., Diruggiero, J., Forry, S. P., Hasan, N. A. & 16 others, , Nov 5 2018, In : Microbiome. 6, 1, 197.Research output: Contribution to journal › Article
Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V. & Knight, R., Apr 10 2018, In : Nature Medicine. 24, 4, p. 392-400 9 p.Research output: Contribution to journal › Article
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017
Sinha, R., Ahsan, H., Blaser, M., Caporaso, J. G., Carmical, J. R., Chan, A. T., Fodor, A., Gail, M. H., Harris, C. C., Helzlsouer, K., Huttenhower, C., Knight, R., Kong, H. H., Lai, G. Y., Hutchinson, D. L. S., Le Marchand, L., Li, H., Orlich, M. J., Shi, J., Truelove, A. & 7 others, , Nov 26 2018, In : Microbiome. 6, 1, 210.Research output: Contribution to journal › Article
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin
Bokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M., Bolyen, E., Knight, R., Huttley, G. A. & Caporaso, J. G., May 17 2018, In : Microbiome. 6, 1, 90.Research output: Contribution to journal › Article
Qiita: rapid, web-enabled microbiome meta-analysis
Gonzalez, A., Navas-Molina, J. A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A. D., Orchanian, S. B., Sanders, J. G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C. J., Wang, M., Rideout, J. R., Bolyen, E., Dillon, M. & 3 others, , Oct 1 2018, In : Nature Methods. 15, 10, p. 796-798 3 p.Research output: Contribution to journal › Article
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. & Huttenhower, C., Nov 1 2018, In : Nature Methods. 15, 11, p. 962-968 7 p.Research output: Contribution to journal › Article
Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: An open-label study
Kang, D. W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E. L., Roux, S., Sadowsky, M. J., Lipson, K. S., Sullivan, M. B., Caporaso, J. G. & Krajmalnik-Brown, R., 2017, In : Microbiome. 5, 1, 10.Research output: Contribution to journal › Article
Multi-omics analysis of periodontal pocket microbial communities pre- and posttreatment
Califf, K. J., Schwarzberg-Lipson, K., Garg, N., Gibbons, S. M., Caporaso, J. G., Slots, J., Cohen, C., Dorrestein, P. C. & Kelley, S. T., May 1 2017, In : mSystems. 2, 3, e00016.Research output: Contribution to journal › Article
Significant impacts of increasing aridity on the arid soil microbiome
Neilson, J. W., Califf, K., Cardona, C., Copeland, A., Van Treuren, W., Josephson, K. L., Knight, R., Gilbert, J. A., Quade, J., Caporaso, J. G. & Maier, R. M., May 1 2017, In : mSystems. 2, 3, e00195.Research output: Contribution to journal › Article
Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for Illumina amplicon sequencing
Taylor, D. L., Walters, W. A., Lennon, N. J., Bochicchio, J., Krohn, A., Caporaso, J. G. & Pennanen, T., 2016, In : Applied and Environmental Microbiology. 82, 24, p. 7217-7226 10 p.Research output: Contribution to journal › Article
cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
Chase, J. H., Bolyen, E., Rideout, J. R. & Caporaso, J. G., Jan 1 2016, In : mSystems. 1, 1, e00010-15.Research output: Contribution to journal › Article
Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses
Fouquier, J., Rideout, J. R., Bolyen, E., Chase, J., Shiffer, A., McDonald, D., Knight, R., Caporaso, J. G. & Kelley, S. T., 2016, In : Microbiome. 4, 11.Research output: Contribution to journal › Article
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys
Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A. & Knight, R., Jan 1 2016, In : mSystems. 1, 1, e00009-15.Research output: Contribution to journal › Article
Keemei: Cloud-based validation of tabular bioinformatics file formats in Google Sheets
Rideout, J. R., Chase, J. H., Bolyen, E., Ackermann, G., González, A., Knight, R. & Caporaso, J. G., 2016, In : GigaScience. 5, 1, 27.Research output: Contribution to journal › Article
Metagenomics reveals dysbiosis and a potentially pathogenic N. flavescens strain in duodenum of adult celiac patients
D'Argenio, V., Casaburi, G., Precone, V., Pagliuca, C., Colicchio, R., Sarnataro, D., Discepolo, V., Kim, S. M., Russo, I., Del Vecchio Blanco, G., Horner, D. S., Chiara, M., Pesole, G., Salvatore, P., Monteleone, G., Ciacci, C., Caporaso, J. G., Jabrì, B., Salvatore, F. & Sacchetti, L., Jun 1 2016, In : American Journal of Gastroenterology. 111, 6, p. 879-890 12 p.Research output: Contribution to journal › Article
Mockrobiota: A public resource for microbiome bioinformatics benchmarking
Bokulich, N. A., Rideout, J. R., Mercurio, W. G., Shiffer, A., Wolfe, B., Maurice, C. F., Dutton, R. J., Turnbaugh, P. J., Knight, R. & Caporaso, J. G., Sep 1 2016, In : mSystems. 1, 5, e00062.Research output: Contribution to journal › Article
Open-Source Sequence Clustering Methods Improve the State Of the Art
Kopylova, E., Navas-Molina, J. A., Mercier, C., Xu, Z. Z., Mahé, F., He, Y., Zhou, H. W., Rognes, T., Caporaso, J. G. & Knight, R., Jan 1 2016, In : mSystems. 1, 1, e00003-15.Research output: Contribution to journal › Article
Phylogenetic organization of bacterial activity
Morrissey, E. M., Mau, R. L., Schwartz, E., Caporaso, J. G., Dijkstra, P., van Gestel, N., Koch, B. J., Liu, C. M., Hayer, M., McHugh, T. A., Marks, J. C., Price, L. B. & Hungate, B. A., Mar 4 2016, (Accepted/In press) In : ISME Journal.Research output: Contribution to journal › Article
Reduced epithelial Na+/H+exchange drives gut microbial dysbiosis and promotes inflammatory response in T cell-mediated murine colitis
Laubitz, D., Harrison, C. A., Midura-Kiela, M. T., Ramalingam, R., Larmonier, C. B., Chase, J. H., Caporaso, J. G., Besselsen, D. G., Ghishan, F. K. & Kiela, P. R., Apr 1 2016, In : PLoS One. 11, 4, e0152044.Research output: Contribution to journal › Article
A state-space modeling approach to estimating canopy conductance and associated uncertainties from sap flux density data
Bell, D. M., Ward, E. J., Oishi, A. C., Oren, R., Flikkema, P. G. & Clark, J. S., Jun 1 2015, In : Tree Physiology. 35, 7, p. 792-802 11 p.Research output: Contribution to journal › Article
Automated Fault Location and Isolation in Distribution Grids with Distributed Control and Unreliable Communication
Kashyap, N., Yang, C. W., Sierla, S. & Flikkema, P. G., 2015, In : IEEE Transactions on Industrial Electronics. 62, 4, p. 2612-2619 8 p., 7000540.Research output: Contribution to journal › Article
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota
Smith, C. C. R., Snowberg, L. K., Caporaso, J. G., Knight, R. & Bolnick, D. I., Nov 1 2015, In : ISME Journal. 9, 11, p. 2515-2526 12 p.Research output: Contribution to journal › Article
Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: Follow-up of a randomized controlled trial
Holscher, H. D., Caporaso, J. G., Hooda, S., Brulc, J. M., Fahey, G. C. & Swanson, K. S., Jan 1 2015, In : American Journal of Clinical Nutrition. 101, 1, p. 55-64 10 p.Research output: Contribution to journal › Article
From rare to dominant: A fine-tuned soil bacterial bloom during petroleum hydrocarbon bioremediation
Fuentes, S., Barra, B., Caporaso, J. G. & Seeger, M., 2015, In : Applied and Environmental Microbiology. 82, 3, p. 888-896 9 p.Research output: Contribution to journal › Article
Genomic Standards Consortium Projects
Field, D., Sterk, P., Kottmann, R., Smet, J. W., Amaral-Zettler, L., Cochrane, G., Cole, J. R., Davies, N., Dawyndt, P., Garrity, G. M., Gilbert, J. A., Glöckner, F. O., Hirschman, L., Klenk, H. P., Knight, R., Kyrpides, N., Meyer, F., Karsch-Mizrachi, I., Morrison, N., Robbins, R. & 9 others, , Oct 30 2015, (Accepted/In press) In : Standards in Genomic Sciences.Research output: Contribution to journal › Article
Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone
Kang, D. W., DiBaise, J. K., Ilhan, Z. E., Crowell, M. D., Rideout, J. R., Caporaso, J. G., Rittmann, B. E. & Krajmalnik-Brown, R., Jun 1 2015, In : Anaerobe. 33, p. 33-41 9 p.Research output: Contribution to journal › Article
Quantitative microbial ecology through stable isotope probing
Hungate, B. A., Mau, R. L., Schwartz, E., Caporaso, J. G., Dijkstra, P., van Gestel, N., Koch, B. J., Liu, C. M., McHugh, T. A., Marks, J. C., Morrissey, E. M. & Price, L. B., 2015, In : Applied and Environmental Microbiology. 81, 21, p. 7570-7581 12 p.Research output: Contribution to journal › Article
The role of curcumin in modulating colonic microbiota during colitis and colon cancer prevention
Mcfadden, R. M. T., Larmonier, C. B., Shehab, K. W., Midura-Kiela, M., Ramalingam, R., Harrison, C. A., Besselsen, D. G., Chase, J. H., Caporaso, J. G., Jobin, C., Ghishan, F. K. & Kiela, P. R., Jul 25 2015, In : Inflammatory Bowel Diseases. 21, 11, p. 2483-2494 12 p.Research output: Contribution to journal › Article
Advancing the microbiome research community
Huttenhower, C., Knight, R., Brown, C. T., Caporaso, J. G., Clemente, J. C., Gevers, D., Franzosa, E. A., Kelley, S. T., Knights, D., Ley, R. E., Mahurkar, A., Ravel, J. & White, O., Oct 9 2014, In : Cell. 159, 2, p. 227-230 4 p.Research output: Contribution to journal › Article
A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples
Rothrock, M. J., Hiett, K. L., Gamble, J., Caudill, A. C., Cicconi-Hogan, K. M. & Caporaso, J. G., 2014, In : Journal of visualized experiments : JoVE. 94Research output: Contribution to journal › Article
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity
Shade, A., Jones, S. E., Caporaso, J. G., Handelsman, J., Knight, R., Fierer, N. & Gilbert, J. A., Jul 15 2014, In : mBio. 5, 4, e01371-14.Research output: Contribution to journal › Article
Conducting a microbiome study
Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R. & Ley, R. E., Jul 17 2014, In : Cell. 158, 2, p. 250-262 13 p.Research output: Contribution to journal › Article
Individual diet has sex-dependent effects on vertebrate gut microbiota
Bolnick, D. I., Snowberg, L. K., Hirsch, P. E., Lauber, C. L., Org, E., Parks, B., Lusis, A. J., Knight, R., Caporaso, J. G. & Svanbäck, R., Jul 29 2014, In : Nature Communications. 5, 4500.Research output: Contribution to journal › Article
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)
Bolnick, D. I., Snowberg, L. K., Hirsch, P. E., Lauber, C. L., Knight, R., Caporaso, J. G. & Svanbäck, R., 2014, In : Ecology Letters. 17, 8, p. 979-987 9 p.Research output: Contribution to journal › Article
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity
Bolnick, D. I., Snowberg, L. K., Caporaso, J. G., Lauber, C., Knight, R. & Stutz, W. E., Oct 1 2014, In : Molecular Ecology. 23, 19, p. 4831-4845 15 p.Research output: Contribution to journal › Article
PH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils
Feng, Y., Grogan, P., Caporaso, J. G., Zhang, H., Lin, X., Knight, R. & Chu, H., 2014, In : Soil Biology and Biochemistry. 74, p. 193-200 8 p.Research output: Contribution to journal › Article
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
Rideout, J. R., He, Y., Navas-Molina, J. A., Walters, W. A., Ursell, L. K., Gibbons, S. M., Chase, J., McDonald, D., Gonzalez, A., Robbins-Pianka, A., Clemente, J. C., Gilbert, J. A., Huse, S. M., Zhou, H. W., Knight, R. & Caporaso, J. G., 2014, In : PeerJ. 2014, 1, e545.Research output: Contribution to journal › Article
The large-scale blast score ratio (LS-BSR) pipeline: A method to rapidly compare genetic content between bacterial genomes
Sahl, J. W., Caporaso, J. G., Rasko, D. A. & Keim, P. S., 2014, In : PeerJ. 2014, 1, e332.Research output: Contribution to journal › Article
The personal human oral microbiome obscures the effects of treatment on periodontal disease
Schwarzberg, K., Le, R., Bharti, B., Lindsay, S., Casaburi, G., Salvatore, F., Saber, M. H., Alonaizan, F., Slots, J., Gottlieb, R. A., Caporaso, J. G. & Kelley, S. T., Jan 29 2014, In : PLoS One. 9, 1, e86708.Research output: Contribution to journal › Article
A meta-analysis of changes in bacterial and archaeal communities with time
Shade, A., Caporaso, J. G., Handelsman, J., Knight, R. & Fierer, N., Aug 2013, In : ISME Journal. 7, 8, p. 1493-1506 14 p.Research output: Contribution to journal › Article
Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)
Hewitt, K. M., Mannino, F. L., Gonzalez, A., Chase, J. H., Caporaso, J. G., Knight, R. & Kelley, S. T., Jan 29 2013, In : PLoS One. 8, 1, e54703.Research output: Contribution to journal › Article
Cohabiting family members share microbiota with one another and with their dogs
Song, S. J., Lauber, C., Costello, E. K., Lozupone, C. A., Humphrey, G., Berg-Lyons, D., Caporaso, J. G., Knights, D., Clemente, J. C., Nakielny, S., Gordon, J. I., Fierer, N. & Knight, R., Apr 16 2013, In : eLife. 2013, 2, e00458.Research output: Contribution to journal › Article
Collaborative cloud-enabled tools allow rapid, reproducible biological insights
Ragan-Kelley, B., Walters, W. A., McDonald, D., Riley, J., Granger, B. E., Gonzalez, A., Knight, R., Perez, F. & Caporaso, J. G., Mar 2013, In : ISME Journal. 7, 3, p. 461-464 4 p.Research output: Contribution to journal › Article
Cyber-eco technology: Engineering of ecological systems
Flikkema, P. G., 2013, In : Proceedings of the IEEE. 101, 5, p. 1031-1033 3 p., 6504492.Research output: Contribution to journal › Article