J. Gregory Caporaso

Department of Biological Sciences, Northern Arizona University

Affiliated withNorthern Arizona University

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 29	2014

Other Publications

Article	Year
Origins of the genetic code: the escaped triplet theory. Annual review of biochemistry\| PubMed ID: 15952885	2005
Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. Journal of molecular evolution\| PubMed ID: 16211428	2005
MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics (Oxford, England)\| PubMed ID: 17495998	2007
PyCogent: a toolkit for making sense from sequence. Genome biology\| PubMed ID: 17708774	2007
Rapid pattern development for concept recognition systems: application to point mutations. Journal of bioinformatics and computational biology\| PubMed ID: 18172927	2007
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing\| PubMed ID: 18229722	2008
Concept recognition for extracting protein interaction relations from biomedical text. Genome biology\| PubMed ID: 18834500	2008
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics. BMC evolutionary biology\| PubMed ID: 19055758	2008
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (Oxford, England)\| PubMed ID: 19914921	2010
QIIME allows analysis of high-throughput community sequencing data. Nature methods\| PubMed ID: 20383131	2010
Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME journal\| PubMed ID: 20445636	2010
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20534432	2011
Examining the global distribution of dominant archaeal populations in soil. The ISME journal\| PubMed ID: 21085198	2011
Bacterial communities associated with the lichen symbiosis. Applied and environmental microbiology\| PubMed ID: 21169444	2011
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics (Oxford, England)\| PubMed ID: 21349862	2011
Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PloS one\| PubMed ID: 21383980	2011
New insight into the diversity of life's building blocks: evenness, not variance. Astrobiology\| PubMed ID: 21417743	2011
Moving pictures of the human microbiome. Genome biology\| PubMed ID: 21624126	2011
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. The ISME journal\| PubMed ID: 21716311	2012
Defining seasonal marine microbial community dynamics. The ISME journal\| PubMed ID: 21850055	2012
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Bioinformatics (Oxford, England)\| PubMed ID: 21903626	2011
The Western English Channel contains a persistent microbial seed bank. The ISME journal\| PubMed ID: 22071345	2012
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]\| PubMed ID: 22161565	2011
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. The ISME journal\| PubMed ID: 22170427	2012
Sequencing our way towards understanding global eukaryotic biodiversity. Trends in ecology & evolution\| PubMed ID: 22244672	2012
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil biology & biochemistry\| PubMed ID: 22267877	2011
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal\| PubMed ID: 22402401	2012
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. The Journal of allergy and clinical immunology\| PubMed ID: 22541361	2012
Human gut microbiome viewed across age and geography. Nature\| PubMed ID: 22699611	2012
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. The ISME journal\| PubMed ID: 22832344	2013
Collaborative cloud-enabled tools allow rapid, reproducible biological insights. The ISME journal\| PubMed ID: 23096404	2013
Diversity, distribution and sources of bacteria in residential kitchens. Environmental microbiology\| PubMed ID: 23171378	2013
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current protocols in microbiology\| PubMed ID: 23184592	2012
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature methods\| PubMed ID: 23202435	2013
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23236140	2012
Bacterial diversity in two Neonatal Intensive Care Units (NICUs). PloS one\| PubMed ID: 23372757	2013
From molecules to dynamic biological communities. Biology & philosophy\| PubMed ID: 23483075	2013
Evidence for a persistent microbial seed bank throughout the global ocean. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23487761	2013
A meta-analysis of changes in bacterial and archaeal communities with time. The ISME journal\| PubMed ID: 23575374	2013
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience\| PubMed ID: 23587224	2012
Cohabiting family members share microbiota with one another and with their dogs. eLife\| PubMed ID: 23599893	2013
The Ecology of Microbial Communities Associated with Macrocystis pyrifera. PloS one\| PubMed ID: 23840715	2013
Meeting report: fungal its workshop (october 2012). Standards in genomic sciences\| PubMed ID: 23961317	2013
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology\| PubMed ID: 23975157	2013
Advancing our understanding of the human microbiome using QIIME. Methods in enzymology\| PubMed ID: 24060131	2013
The personal human oral microbiome obscures the effects of treatment on periodontal disease. PloS one\| PubMed ID: 24489772	2014
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ\| PubMed ID: 24749011	2014
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecology letters\| PubMed ID: 24847735	2014
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Molecular ecology\| PubMed ID: 24975397	2014
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio\| PubMed ID: 25028427	2014
Conducting a microbiome study. Cell\| PubMed ID: 25036628	2014
Individual diet has sex-dependent effects on vertebrate gut microbiota. Nature communications\| PubMed ID: 25072318	2014
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ\| PubMed ID: 25177538	2014
Advancing the microbiome research community. Cell\| PubMed ID: 25303518	2014