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2020

Microbiotyping the Sinonasal Microbiome

Bassiouni, A., Paramasivan, S., Shiffer, A., Dillon, M. R., Cope, E. K., Cooksley, C., Ramezanpour, M., Moraitis, S., Ali, M. J., Bleier, B. S., Callejas, C., Cornet, M. E., Douglas, R. G., Dutra, D., Georgalas, C., Harvey, R. J., Hwang, P. H., Luong, A. U., Schlosser, R. J., Tantilipikorn, P. & 5 others, Tewfik, M. A., Vreugde, S., Wormald, P. J., Caporaso, J. G. & Psaltis, A. J., Apr 8 2020, In : Frontiers in Cellular and Infection Microbiology. 10, 137.

Research output: Contribution to journalArticle

Open Access

Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran

Vogtmann, E., Han, Y., Caporaso, J. G., Bokulich, N., Mohamadkhani, A., Moayyedkazemi, A., Hua, X., Kamangar, F., Wan, Y., Suman, S., Zhu, B., Hutchinson, A., Dagnall, C., Jones, K., Hicks, B., Shi, J., Malekzadeh, R., Abnet, C. C. & Pourshams, A., Jan 1 2020, In : Cancer Medicine. 9, 2, p. 797-806 10 p.

Research output: Contribution to journalArticle

Open Access

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

Kaplan, I., Bokulich, N. A., Caporaso, J. G., Enders, L. S., Ghanem, W. & Ingerslew, K. S., Jan 1 2020, (Accepted/In press) In : Evolutionary Applications.

Research output: Contribution to journalArticle

Open Access

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Estaki, M., Jiang, L., Bokulich, N. A., McDonald, D., González, A., Kosciolek, T., Martino, C., Zhu, Q., Birmingham, A., Vázquez-Baeza, Y., Dillon, M. R., Bolyen, E., Caporaso, J. G. & Knight, R., Jun 1 2020, In : Current protocols in bioinformatics. 70, 1, p. e100

Research output: Contribution to journalArticle

Open Access

The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology

Paramasivan, S., Bassiouni, A., Shiffer, A., Dillon, M. R., Cope, E. K., Cooksley, C., Ramezanpour, M., Moraitis, S., Ali, M. J., Bleier, B., Callejas, C., Cornet, M. E., Douglas, R. G., Dutra, D., Georgalas, C., Harvey, R. J., Hwang, P. H., Luong, A. U., Schlosser, R. J., Tantilipikorn, P. & 5 others, Tewfik, M. A., Vreugde, S., Wormald, P. J., Caporaso, J. G. & Psaltis, A. J., Jan 1 2020, (Accepted/In press) In : Allergy: European Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticle

2019

Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development

Pearson, T., 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 journalArticle

Open Access
5 Scopus citations

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 journalArticle

Open Access
41 Scopus citations

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 journalArticle

Open Access

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 journalArticle

Open Access
1 Scopus citations

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 journalArticle

2018

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, Kralj, J., Luethy, P. M., Milton, D. K., Ondov, B. D., Preheim, S., Ratnayake, S., Rogers, S. M., Rosovitz, M. J., Sakowski, E. G., Schliebs, N. O., Sommer, D. D., Ternus, K. L., Uritskiy, G., Zhang, S. X., Pop, M. & Treangen, T. J., Nov 5 2018, In : Microbiome. 6, 1, 197.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

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 journalArticle

235 Scopus citations

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, Verma, M., Vogtmann, E., White, O., Willett, W., Zheng, W., Mahabir, S. & Abnet, C., Nov 26 2018, In : Microbiome. 6, 1, 210.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

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. & Gregory Caporaso, J., May 17 2018, In : Microbiome. 6, 1, 90.

Research output: Contribution to journalArticle

179 Scopus citations

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, Caporaso, J. G., Dorrestein, P. C. & Knight, R., Oct 1 2018, In : Nature Methods. 15, 10, p. 796-798 3 p.

Research output: Contribution to journalArticle

66 Scopus citations

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 journalArticle

95 Scopus citations
2017

A communal catalogue reveals Earth's multiscale microbial diversity

Earth Microbiome Project Consortium, Nov 23 2017, In : Nature. 551, 7681, p. 457-463 7 p.

Research output: Contribution to journalArticle

362 Scopus citations

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., Jan 1 2017, In : Microbiome. 5, 1, 10.

Research output: Contribution to journalArticle

274 Scopus citations

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 journalArticle

14 Scopus citations

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 journalArticle

23 Scopus citations
2016

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., Jan 1 2016, In : Applied and Environmental Microbiology. 82, 24, p. 7217-7226 10 p.

Research output: Contribution to journalArticle

84 Scopus citations

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 journalArticle

4 Scopus citations

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., Jan 1 2016, In : Microbiome. 4, 11.

Research output: Contribution to journalArticle

7 Scopus citations

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 journalArticle

255 Scopus citations

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 journalArticle

4 Scopus citations

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, G. J., 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 journalArticle

53 Scopus citations

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 journalArticle

28 Scopus citations

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 journalArticle

71 Scopus citations

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 journalArticle

37 Scopus citations

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 journalArticle

17 Scopus citations
2015

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 journalArticle

12 Scopus citations

Automated Fault Location and Isolation in Distribution Grids with Distributed Control and Unreliable Communication

Kashyap, N., Yang, C. W., Sierla, S. & Flikkema, P. G., Apr 2015, In : IEEE Transactions on Industrial Electronics. 62, 4, p. 2612-2619 8 p., 7000540.

Research output: Contribution to journalArticle

22 Scopus citations

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography

Marzinelli, E. M., Campbell, A. H., Zozaya Valdes, E., Vergés, A., Nielsen, S., Wernberg, T., de Bettignies, T., Bennett, S., Caporaso, J. G., Thomas, T. & Steinberg, P. D., Oct 1 2015, In : Environmental microbiology.

Research output: Contribution to journalArticle

50 Scopus citations

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 journalArticle

82 Scopus citations

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: Follow-up of a randomized controlled trial

Holscher, H. D., Gregory Caporaso, J., 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 journalArticle

62 Scopus citations

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 journalArticle

43 Scopus citations

Genomic standards consortium projects

Field, D., Sterk, P., Kottmann, R., De 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, Gil, I. S., Sansone, S., Schriml, L., Tatusova, T., Ussery, D., Yilmaz, P., White, O., Wooley, J. & Caporaso, G., Oct 30 2015, In : Standards in Genomic Sciences. 9, 3, p. 599-601 3 p.

Research output: Contribution to journalArticle

17 Scopus citations

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 journalArticle

23 Scopus citations

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 journalArticle

73 Scopus citations

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 journalArticle

51 Scopus citations
2014

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. & Gregory Caporaso, J., Dec 10 2014, In : Journal of Visualized Experiments. 94, e52161.

Research output: Contribution to journalArticle

10 Scopus citations

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

Shade, A., Jones, S. E., Gregory Caporaso, J., Handelsman, J., Knight, R., Fierer, N. & Gilbert, J. A., Jul 15 2014, In : mBio. 5, 4, e01371-14.

Research output: Contribution to journalArticle

205 Scopus citations

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 journalArticle

220 Scopus citations

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., Aug 2014, In : Ecology Letters. 17, 8, p. 979-987 9 p.

Research output: Contribution to journalArticle

107 Scopus citations

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 journalArticle

71 Scopus citations

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., Jul 2014, In : Soil Biology and Biochemistry. 74, p. 193-200 8 p.

Research output: Contribution to journalArticle

38 Scopus citations

Process modeling for soil moisture using sensor network data

Ghosh, S., Bell, D. M., Clark, J. S., Gelfand, A. E. & Flikkema, P. G., Jan 1 2014, In : Statistical Methodology. 17, C, p. 99-112 14 p.

Research output: Contribution to journalArticle

5 Scopus citations

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. & Gregory Caporaso, J., Jan 1 2014, In : PeerJ. 2014, 1, e545.

Research output: Contribution to journalArticle

278 Scopus citations

Temporal variability is a personalized feature of the human microbiome

Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R. A., Domogala, D., Chase, J., Leff, J. W., Vázquez-Baeza, Y., Gonzalez, A., Knight, R., Dunn, R. R. & Fierer, N., Jan 1 2014, In : Genome biology. 15, 12, 1 p.

Research output: Contribution to journalArticle

148 Scopus citations

The large-scale blast score ratio (LS-BSR) pipeline: A method to rapidly compare genetic content between bacterial genomes

Sahl, J. W., Gregory Caporaso, J., Rasko, D. A. & Keim, P., Jan 1 2014, In : PeerJ. 2014, 1, e332.

Research output: Contribution to journalArticle

90 Scopus citations