Research Output

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 Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

Xavier, J. B., Young, V. B., Skufca, J., Ginty, F., Testerman, T., Pearson, A. T., Macklin, P., Mitchell, A., Shmulevich, I., Xie, L., Caporaso, J. G., Crandall, K. A., Simone, N. L., Godoy-Vitorino, F., Griffin, T. J., Whiteson, K. L., Gustafson, H. H., Slade, D. J., Schmidt, T. M., Walther-Antonio, M. R. S. & 10 others, Korem, T., Webb-Robertson, B. J. M., Styczynski, M. P., Johnson, W. E., Jobin, C., Ridlon, J. M., Koh, A. Y., Yu, M., Kelly, L. & Wargo, J. A., Mar 2020, In : Trends in Cancer. 6, 3, p. 192-204 13 p.

Research output: Contribution to journalReview article

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

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)

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., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., Sep 1 2019, In : Nature Biotechnology. 37, 9, 1 p.

Research output: Contribution to journalComment/debate

Open Access
2 Scopus citations

Control and Optimization of Energy Efficiency in Small-Footprint Embedded Systems: A Coupled Hybrid Systems Model

Porter, C., Yamamoto, K. & Flikkema, P. G., Mar 2019, Proceedings of 2019 SICE International Symposium on Control Systems, SICE ISCS 2019. Institute of Electrical and Electronics Engineers Inc., p. 1-8 8 p. 8758755. (Proceedings of 2019 SICE International Symposium on Control Systems, SICE ISCS 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Documentation as a cross-cutting concern of sofware

Palmer, J. D. & McAddis, N., Oct 4 2019, SIGDOC 2019 - Proceedings of the 37th ACM International Conference on the Design of Communication. Association for Computing Machinery, Inc, 18. (SIGDOC 2019 - Proceedings of the 37th ACM International Conference on the Design of Communication).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins

Stone, N. E., Nunnally, A. E., Jimenez, V., Cope, E. K., Sahl, J. W., Sheridan, K., Hornstra, H. M., Vinocur, J., Settles, E. W., Headley, K. C., Williamson, C. H. D., Rideout, J. R., Bolyen, E., Caporaso, J. G., Terriquez, J., Monroy, F. P., Busch, J. D., Keim, P. S. & Wagner, D. M., Jan 1 2019, In : Anaerobe.

Research output: Contribution to journalReview article

Open Access
4 Scopus citations

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

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., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., Aug 1 2019, In : Nature Biotechnology. 37, 8, p. 852-857 6 p.

Research output: Contribution to journalLetter

234 Scopus citations

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

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, Zhu, Q., Caporaso, J. G. & Dorrestein, P. C., Jul 1 2018, In : Nature Reviews Microbiology. 16, 7, p. 410-422 13 p.

Research output: Contribution to journalReview article

185 Scopus citations

Cellular mobile telephony

Flikkema, P. G., Jan 1 2018, The RF and Microwave Handbook: RF and Microwave Applications and Systems. CRC Press, p. 3-1-3-17

Research output: Chapter in Book/Report/Conference proceedingChapter

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

Support of distributed ecological experiments via closed-loop environmental control

Knapp, J. D., Middleton, M., Heinrich, P., Whipple, A. V. & Flikkema, P. G., Apr 6 2018, 2017 IEEE Conference on Technologies for Sustainability, SusTech 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-January. p. 1-6 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Adapting processor architectures for the periphery of the IoT nervous system

Flikkema, P. G. & Cambou, B., Feb 6 2017, 2016 IEEE 3rd World Forum on Internet of Things, WF-IoT 2016. Institute of Electrical and Electronics Engineers Inc., p. 615-620 6 p. 7845427

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Design and implementation of an energy-neutral solar energy system for wireless sensor-actuator nodes

Knapp, J. D. & Flikkema, P. G., Aug 23 2017, GIoTS 2017 - Global Internet of Things Summit, Proceedings. Institute of Electrical and Electronics Engineers Inc., 8016244

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Development of a datalogger for assessment of solar energy harvesting in submarine environments

Bruce, T., Morris, C., Adoram-Kershner, L., Holser, R., Costa, D., Flikkema, P. G. & Shafer, M. W., Dec 19 2017, OCEANS 2017 � Anchorage. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 1-9 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 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

Modeling and testing solar power for globally migrating submarine systems

Adoram-Kershner, L., Bruce, T., Morris, C., Holser, R., Costa, D., Flikkema, P. G. & Shafer, M. W., Dec 19 2017, OCEANS 2017 � Anchorage. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 1-9 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 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

Self-adaptive and resilient urban networking infrastructure for disasters and smart city services

Flikkema, P. G. & Vigil-Hayes, M., Jul 1 2017, Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017. Nie, J-Y., Obradovic, Z., Suzumura, T., Ghosh, R., Nambiar, R., Wang, C., Zang, H., Baeza-Yates, R., Baeza-Yates, R., Hu, X., Kepner, J., Cuzzocrea, A., Tang, J. & Toyoda, M. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 4074-4079 6 p. (Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017; vol. 2018-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

The NAU/CQUPT 3+1 program in electrical engineering

Mlsna, P. A., Cheng, F., Scott, D. R., Yang, J., Li, G. & Zhou, X., Jun 28 2017, 2017 ASEE International Forum. American Society for Engineering Education

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Towards automated composition of heterogeneous tests for cyber-physical systems

Groce, A., Flikkema, P. & Holmes, J., Jul 13 2017, TECPS 2017 - Proceedings of the 1st ACM SIGSOFT International Workshop on Testing Embedded and Cyber-Physical Systems, co-located with ISSTA 2017. Yu, T. & Marinov, D. (eds.). Association for Computing Machinery, Inc, p. 12-15 4 p. (TECPS 2017 - Proceedings of the 1st ACM SIGSOFT International Workshop on Testing Embedded and Cyber-Physical Systems, co-located with ISSTA 2017).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

When things are sensors for cloud AI: Protecting privacy through data collection transparency in the age of digital assistants

Flikkema, P. G. & Cambou, B., Aug 23 2017, GIoTS 2017 - Global Internet of Things Summit, Proceedings. Institute of Electrical and Electronics Engineers Inc., 8016284

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 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

A multi-round double auction mechanism for local energy grids with distributed and centralized resources

Flikkema, P. G., Nov 15 2016, Proceedings - 2016 IEEE 25th International Symposium on Industrial Electronics, ISIE 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-November. p. 672-677 6 p. 7744970

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

A Step Forward to Empower Global Microbiome Research Through Local Leadership

The Working Group Supporting the INCT Microbiome, Oct 1 2016, In : Trends in Microbiology. 24, 10, p. 767-771 5 p.

Research output: Contribution to journalComment/debate

Open Access
5 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

Geography and location are the primary drivers of office microbiome composition

Chase, J., Fouquier, J., Zare, M., Sonderegger, D. L., Knight, R., Kelley, S. T., Siegel, J. & Caporaso, J. G., Mar 1 2016, In : mSystems. 1, 2, e00022-16.

Research output: Contribution to journalReview article

46 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

No change in the mucosal gut microbiome is associated with celiac disease-specific microbiome alteration in adult 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., Nov 1 2016, In : American Journal of Gastroenterology. 111, 11, p. 1659-1661 3 p.

Research output: Contribution to journalLetter

10 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