Department of Biological Sciences,
Center for Microbial Genetics and Genomics,
Department of Biological Sciences, Center for Microbial Genetics and Genomics
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Origins of the genetic code: the escaped triplet theory.
Annual review of biochemistry , 2005 | Pubmed ID: 15952885
Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code.
Journal of molecular evolution Nov, 2005 | Pubmed ID: 16211428
MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinformatics (Oxford, England) Jul, 2007 | Pubmed ID: 17495998
PyCogent: a toolkit for making sense from sequence.
Genome biology , 2007 | Pubmed ID: 17708774
Rapid pattern development for concept recognition systems: application to point mutations.
Journal of bioinformatics and computational biology Dec, 2007 | Pubmed ID: 18172927
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing , 2008 | Pubmed ID: 18229722
Concept recognition for extracting protein interaction relations from biomedical text.
Genome biology , 2008 | Pubmed ID: 18834500
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.
BMC evolutionary biology , 2008 | Pubmed ID: 19055758
PyNAST: a flexible tool for aligning sequences to a template alignment.
Bioinformatics (Oxford, England) Jan, 2010 | Pubmed ID: 19914921
QIIME allows analysis of high-throughput community sequencing data.
Nature methods May, 2010 | Pubmed ID: 20383131
Soil bacterial and fungal communities across a pH gradient in an arable soil.
The ISME journal Oct, 2010 | Pubmed ID: 20445636
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 Mar, 2011 | Pubmed ID: 20534432
Examining the global distribution of dominant archaeal populations in soil.
The ISME journal May, 2011 | Pubmed ID: 21085198
Bacterial communities associated with the lichen symbiosis.
Applied and environmental microbiology Feb, 2011 | Pubmed ID: 21169444
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Bioinformatics (Oxford, England) Apr, 2011 | Pubmed ID: 21349862
Host-associated and free-living phage communities differ profoundly in phylogenetic composition.
PloS one , 2011 | Pubmed ID: 21383980
New insight into the diversity of life's building blocks: evenness, not variance.
Astrobiology Apr, 2011 | Pubmed ID: 21417743
Moving pictures of the human microbiome.
Genome biology , 2011 | Pubmed ID: 21624126
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.
The ISME journal Jan, 2012 | Pubmed ID: 21716311
Defining seasonal marine microbial community dynamics.
The ISME journal Feb, 2012 | Pubmed ID: 21850055
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.
Bioinformatics (Oxford, England) Nov, 2011 | Pubmed ID: 21903626
The Western English Channel contains a persistent microbial seed bank.
The ISME journal Jun, 2012 | Pubmed ID: 22071345
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Dec, 2011 | Pubmed ID: 22161565
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.
The ISME journal Jul, 2012 | Pubmed ID: 22170427
Sequencing our way towards understanding global eukaryotic biodiversity.
Trends in ecology & evolution Apr, 2012 | Pubmed ID: 22244672
The under-recognized dominance of Verrucomicrobia in soil bacterial communities.
Soil biology & biochemistry Jul, 2011 | Pubmed ID: 22267877
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
The ISME journal Aug, 2012 | Pubmed ID: 22402401
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.
The Journal of allergy and clinical immunology May, 2012 | Pubmed ID: 22541361
Human gut microbiome viewed across age and geography.
Nature Jun, 2012 | Pubmed ID: 22699611
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.
The ISME journal Jan, 2013 | Pubmed ID: 22832344
Collaborative cloud-enabled tools allow rapid, reproducible biological insights.
The ISME journal Mar, 2013 | Pubmed ID: 23096404
Diversity, distribution and sources of bacteria in residential kitchens.
Environmental microbiology Feb, 2013 | Pubmed ID: 23171378
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.
Current protocols in microbiology Nov, 2012 | Pubmed ID: 23184592
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Nature methods Jan, 2013 | Pubmed ID: 23202435
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 Dec, 2012 | Pubmed ID: 23236140
Bacterial diversity in two Neonatal Intensive Care Units (NICUs).
PloS one , 2013 | Pubmed ID: 23372757
From molecules to dynamic biological communities.
Biology & philosophy Mar, 2013 | Pubmed ID: 23483075
Evidence for a persistent microbial seed bank throughout the global ocean.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2013 | Pubmed ID: 23487761
A meta-analysis of changes in bacterial and archaeal communities with time.
The ISME journal Aug, 2013 | Pubmed ID: 23575374
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
GigaScience , 2012 | Pubmed ID: 23587224
Cohabiting family members share microbiota with one another and with their dogs.
eLife , 2013 | Pubmed ID: 23599893
The Ecology of Microbial Communities Associated with Macrocystis pyrifera.
PloS one , 2013 | Pubmed ID: 23840715
Meeting report: fungal its workshop (october 2012).
Standards in genomic sciences Apr, 2013 | Pubmed ID: 23961317
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.
Nature biotechnology Sep, 2013 | Pubmed ID: 23975157
Advancing our understanding of the human microbiome using QIIME.
Methods in enzymology , 2013 | Pubmed ID: 24060131
The personal human oral microbiome obscures the effects of treatment on periodontal disease.
PloS one , 2014 | Pubmed ID: 24489772
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.
PeerJ , 2014 | Pubmed ID: 24749011
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).
Ecology letters Aug, 2014 | Pubmed ID: 24847735
Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.
Molecular ecology Oct, 2014 | Pubmed ID: 24975397
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.
mBio , 2014 | Pubmed ID: 25028427
Conducting a microbiome study.
Cell Jul, 2014 | Pubmed ID: 25036628
Individual diet has sex-dependent effects on vertebrate gut microbiota.
Nature communications , 2014 | Pubmed ID: 25072318
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.
PeerJ , 2014 | Pubmed ID: 25177538
Advancing the microbiome research community.
Cell Oct, 2014 | Pubmed ID: 25303518
Michael J. Rothrock Jr.1,
Kelli L. Hiett2,
John Gamble3,
Andrew C. Caudill4,
Kellie M. Cicconi-Hogan1,
J. Gregory Caporaso5
1Egg Safety and Quality Research Unit, USDA-Agricultural Research Service,
2Poultry Microbiological Safety and Processing Research Unit, USDA-Agricultural Research Service,
3Department of Biochemistry and Biophysics, Oregon State University,
4College of Public Health, University of Georgia,
5Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University
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