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- Publications
- Influence
QIIME allows analysis of high-throughput community sequencing data
- J. Caporaso, Justin Kuczynski, +24 authors R. Knight
- Biology, Medicine
- Nature Methods
- 1 May 2010
Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of… Expand
PyNAST: a flexible tool for aligning sequences to a template alignment
- J. Caporaso, K. Bittinger, F. Bushman, T. Z. DeSantis, G. Andersen, R. Knight
- Computer Science, Medicine
- Bioinform.
- 13 November 2009
TLDR
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- M. Langille, J. Zaneveld, +9 authors C. Huttenhower
- Biology, Medicine
- Nature Biotechnology
- 25 August 2013
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here… Expand
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
- N. A. Bokulich, S. Subramanian, +5 authors J. Caporaso
- Biology, Medicine
- Nature Methods
- 21 November 2012
High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities.… Expand
Human gut microbiome viewed across age and geography
- T. Yatsunenko, F. Rey, +18 authors J. Gordon
- Biology, Medicine
- Nature
- 22 March 2012
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal… Expand
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
- J. Caporaso, Christian L. Lauber, +11 authors R. Knight
- Biology, Medicine
- The ISME Journal
- 8 March 2012
DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon… Expand
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
- J. Caporaso, Christian L. Lauber, +5 authors R. Knight
- Biology, Medicine
- Proceedings of the National Academy of Sciences
- 3 June 2010
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the… Expand
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- E. Bolyen, J. Rideout, +109 authors J. Caporaso
- Engineering, Medicine
- Nature Biotechnology
- 1 August 2019
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and… Expand
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
- N. Fierer, J. W. Leff, +7 authors J. Caporaso
- Biology, Medicine
- Proceedings of the National Academy of Sciences
- 10 December 2012
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for… Expand
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
- Justin Kuczynski, J. Stombaugh, W. Walters, A. González, J. Caporaso, R. Knight
- Biology, Medicine
- Current protocols in bioinformatics
- 1 December 2011
QIIME (canonically pronounced “chime”) is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to… Expand