Research Output 1991 2019

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
Microbiota
Biotechnology

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

Porter, C., Yamamoto, K. & Flikkema, P. G., Mar 1 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

Hybrid systems
Energy Efficiency
Hybrid Systems
Embedded systems
Embedded Systems

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

Embedded software
Architectural design
Application programming interfaces (API)
Software engineering
3 Citations (Scopus)

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
Dysbiosis
Clostridium difficile
Canidae
Infection
Community-Acquired Infections
3 Citations (Scopus)

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 journalArticle

Open Access
Ursodeoxycholic Acid
Adenoma
Microbiota
Bile Acids and Salts
Gastrointestinal Microbiome
16 Citations (Scopus)

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
Microbiota
Autistic Disorder
Therapeutics
Prevotella
Behavioral Symptoms

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
Microbiota
Temperature
Enterobacteriaceae
rRNA Genes
Gastrointestinal Microbiome
36 Citations (Scopus)

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

Microbiota

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
taxonomy
Taxonomies
Classifiers
classifiers
Databases

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

radiotelemetry
radio telemetry
wildlife
flight
bat
2018
112 Citations (Scopus)

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., May 23 2018, (Accepted/In press) In : Nature Reviews Microbiology. p. 1-13 13 p.

Research output: Contribution to journalArticle

Microbiota
Practice Guidelines
Research Design
Technology
Metagenomics
1 Citation (Scopus)

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
Microbiota
Computational Biology
Metagenomics
Communicable Diseases
Information Dissemination
156 Citations (Scopus)

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

Microbiota
Microbial Genome
Aptitude
Metabolome
Gene Expression Profiling
3 Citations (Scopus)

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
Microbiota
Prospective Studies
Education
Health
National Cancer Institute (U.S.)
97 Citations (Scopus)

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 journalArticle

Genes
Taxes
Benchmarking
Microbiota
Machine Learning
37 Citations (Scopus)

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

Microbiota
Meta-Analysis
Chemical analysis

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

Flikkema, P. G. & Vigil-Hayes, M., Jan 12 2018, Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-January. p. 4074-4079 6 p.

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

Emergency services
Disaster
Networking
Disasters
Infrastructure
53 Citations (Scopus)

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

Metagenome
Genes
Metagenomics
Microbiota
Metabolism

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

Soil moisture
Irrigation
Ecosystems
Crops
Rain
2017
2 Citations (Scopus)

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

Neurology
Hardware
Microcontrollers
Pipelines
Engines
4 Citations (Scopus)

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

Solar energy
Actuators
Sensors
Temperature control
Packaging
1 Citation (Scopus)

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

underwater environment
Energy harvesting
solar energy
Solar energy
wildlife
220 Citations (Scopus)

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 journalArticle

Microbiota
Autistic Disorder
Ecosystem
Therapeutics
Autism Spectrum Disorder
1 Citation (Scopus)

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

solar power
Solar energy
sensor
marine environments
modules
8 Citations (Scopus)

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

Periodontal Pocket
Metagenomics
Firearms
Metabolites
microbial communities
18 Citations (Scopus)

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

arid soils
Microbiota
dry environmental conditions
aridity
Soil

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

electrical engineering
Electrical engineering

Towards automated composition of heterogeneous tests for cyber-physical systems

Groce, A., Flikkema, P. G. & 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. Association for Computing Machinery, Inc, p. 12-15 4 p.

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

Chemical analysis
Gateways (computer networks)
Computer operating systems
Testing
abstraction

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

Transparency
Sensors
Data collection
Sensor
Privacy
2016
68 Citations (Scopus)

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 journalArticle

Soil
soil sampling
ribosomal RNA
gene dosage
Large Ribosome Subunits
5 Citations (Scopus)

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

Economics
Distributed power generation
Telecommunication networks
Availability
Heating
4 Citations (Scopus)

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
Microbiota
Research
4 Citations (Scopus)

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

Transcription
comparative study
Metadata
Mints
Mentha
41 Citations (Scopus)

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

Geography
Microbiota
geography
bacterial communities
Driver
6 Citations (Scopus)

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 journalArticle

Phylogeny
Genes
Genetic Markers
Aptitude
Fungi
197 Citations (Scopus)

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

Microbial Genes
Microbiota
rRNA Genes
internal transcribed spacers
microbial communities
3 Citations (Scopus)

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

Bioinformatics
Computational Biology
Spreadsheets
Research Personnel
Information Storage and Retrieval
45 Citations (Scopus)

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 journalArticle

Dysbiosis
Metagenomics
Celiac Disease
Duodenum
Abdomen
23 Citations (Scopus)

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

Benchmarking
bioinformatics
benchmarking
Microbiota
Bioinformatics
10 Citations (Scopus)

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, J. G., 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

67 Citations (Scopus)

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

Clustering Methods
Clustering algorithms
Open Source
Cluster Analysis
Sequencing
35 Citations (Scopus)

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

Phylogeny
microbial activity
Ecosystem
phylogeny
Bacteria
15 Citations (Scopus)

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

Dysbiosis
T-cells
colitis
Colitis
intestinal microorganisms

Supporting software architecture learning using runtime visualization

Georgas, J., Palmer, J. D. & McCormick, M. J., May 19 2016, Proceedings - 2016 IEEE 29th Conference on Software Engineering Education and Training, CSEEandT 2016. Institute of Electrical and Electronics Engineers Inc., p. 101-110 10 p. 7474472

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

Software architecture
Computer graphics
visualization
Visualization
artifact
2015
3 Citations (Scopus)

An auction-based smart district heating grid

Gulzar, K., Sierla, S., Vyatkin, V., Papakonstantinou, N., Flikkema, P. G. & Yang, C. W., Oct 19 2015, IEEE International Conference on Emerging Technologies and Factory Automation, ETFA. Institute of Electrical and Electronics Engineers Inc., Vol. 2015-October. 7301528

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

District heating
Water pipelines
Cogeneration plants
Space heating
Waste heat
11 Citations (Scopus)

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

sap
Uncertainty
uncertainty
canopy
Soil
20 Citations (Scopus)

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 journalArticle

Electric fault location
Automation
Communication
Telecommunication networks
Intelligent agents
67 Citations (Scopus)

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

Smegmamorpha
Gasterosteidae
intestinal microorganisms
genetic variation
genotype
1 Citation (Scopus)

Drawing Insight from Student Perceptions of Reflective Design Learning

Wilkins, T. V. & Georgas, J., Aug 12 2015, Proceedings - International Conference on Software Engineering. IEEE Computer Society, Vol. 2. p. 253-262 10 p. 7202970

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

Students
Computer science
Software engineering
57 Citations (Scopus)

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 journalArticle

polydextrose
Microbiota
Bacteroidetes
Bacterial Genes
Firearms