J. Gregory Caporaso

Publications

• Advancing the Microbiome Research Community
  Cell. Oct, 2014  |   Pubmed ID: 25303518
• Subsampled Open-reference Clustering Creates Consistent, Comprehensive OTU Definitions and Scales to Billions of Sequences
  PeerJ. 2014  |   Pubmed ID: 25177538
• Individual Diet Has Sex-dependent Effects on Vertebrate Gut Microbiota
  Nature Communications. 2014  |   Pubmed ID: 25072318
• Conducting a Microbiome Study
  Cell. Jul, 2014  |   Pubmed ID: 25036628
• Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
  MBio. 2014  |   Pubmed ID: 25028427
• Major Histocompatibility Complex Class IIb Polymorphism Influences Gut Microbiota Composition and Diversity
  Molecular Ecology. Oct, 2014  |   Pubmed ID: 24975397
• Individuals' Diet Diversity Influences Gut Microbial Diversity in Two Freshwater Fish (threespine Stickleback and Eurasian Perch)
  Ecology Letters. Aug, 2014  |   Pubmed ID: 24847735
• The Large-scale Blast Score Ratio (LS-BSR) Pipeline: a Method to Rapidly Compare Genetic Content Between Bacterial Genomes
  PeerJ. 2014  |   Pubmed ID: 24749011
• The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease
  PloS One. 2014  |   Pubmed ID: 24489772
• Advancing Our Understanding of the Human Microbiome Using QIIME
  Methods in Enzymology. 2013  |   Pubmed ID: 24060131
• Predictive Functional Profiling of Microbial Communities Using 16S RRNA Marker Gene Sequences
  Nature Biotechnology. Sep, 2013  |   Pubmed ID: 23975157
• Meeting Report: Fungal Its Workshop (october 2012)
  Standards in Genomic Sciences. Apr, 2013  |   Pubmed ID: 23961317
• The Ecology of Microbial Communities Associated with Macrocystis Pyrifera
  PloS One. 2013  |   Pubmed ID: 23840715
• Cohabiting Family Members Share Microbiota with One Another and with Their Dogs
  ELife. 2013  |   Pubmed ID: 23599893
• A Meta-analysis of Changes in Bacterial and Archaeal Communities with Time
  The ISME Journal. Aug, 2013  |   Pubmed ID: 23575374
• 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
• From Molecules to Dynamic Biological Communities
  Biology & Philosophy. Mar, 2013  |   Pubmed ID: 23483075
• Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)
  PloS One. 2013  |   Pubmed ID: 23372757
• Quality-filtering Vastly Improves Diversity Estimates from Illumina Amplicon Sequencing
  Nature Methods. Jan, 2013  |   Pubmed ID: 23202435
• Diversity, Distribution and Sources of Bacteria in Residential Kitchens
  Environmental Microbiology. Feb, 2013  |   Pubmed ID: 23171378
• Collaborative Cloud-enabled Tools Allow Rapid, Reproducible Biological Insights
  The ISME Journal. Mar, 2013  |   Pubmed ID: 23096404
• Phylogenetic Stratigraphy in the Guerrero Negro Hypersaline Microbial Mat
  The ISME Journal. Jan, 2013  |   Pubmed ID: 22832344
• The Biological Observation Matrix (BIOM) Format Or: How I Learned to Stop Worrying and Love the Ome-ome
  GigaScience. 2012  |   Pubmed ID: 23587224
• 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
• Using QIIME to Analyze 16S RRNA Gene Sequences from Microbial Communities
  Current Protocols in Microbiology. Nov, 2012  |   Pubmed ID: 23184592
• Human Gut Microbiome Viewed Across Age and Geography
  Nature. Jun, 2012  |   Pubmed ID: 22699611
• 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
• Ultra-high-throughput Microbial Community Analysis on the Illumina HiSeq and MiSeq Platforms
  The ISME Journal. Aug, 2012  |   Pubmed ID: 22402401
• Sequencing Our Way Towards Understanding Global Eukaryotic Biodiversity
  Trends in Ecology & Evolution. Apr, 2012  |   Pubmed ID: 22244672
• Comparison of Illumina Paired-end and Single-direction Sequencing for Microbial 16S RRNA Gene Amplicon Surveys
  The ISME Journal. Jul, 2012  |   Pubmed ID: 22170427
• The Western English Channel Contains a Persistent Microbial Seed Bank
  The ISME Journal. Jun, 2012  |   Pubmed ID: 22071345
• Defining Seasonal Marine Microbial Community Dynamics
  The ISME Journal. Feb, 2012  |   Pubmed ID: 21850055
• Impact of Training Sets on Classification of High-throughput Bacterial 16s RRNA Gene Surveys
  The ISME Journal. Jan, 2012  |   Pubmed ID: 21716311
• The Under-recognized Dominance of Verrucomicrobia in Soil Bacterial Communities
  Soil Biology & Biochemistry. Jul, 2011  |   Pubmed ID: 22267877
• 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
• TopiaryExplorer: Visualizing Large Phylogenetic Trees with Environmental Metadata
  Bioinformatics (Oxford, England). Nov, 2011  |   Pubmed ID: 21903626
• Moving Pictures of the Human Microbiome
  Genome Biology. 2011  |   Pubmed ID: 21624126
• New Insight into the Diversity of Life's Building Blocks: Evenness, Not Variance
  Astrobiology. Apr, 2011  |   Pubmed ID: 21417743
• Host-associated and Free-living Phage Communities Differ Profoundly in Phylogenetic Composition
  PloS One. 2011  |   Pubmed ID: 21383980
• PrimerProspector: De Novo Design and Taxonomic Analysis of Barcoded Polymerase Chain Reaction Primers
  Bioinformatics (Oxford, England). Apr, 2011  |   Pubmed ID: 21349862
• Bacterial Communities Associated with the Lichen Symbiosis
  Applied and Environmental Microbiology. Feb, 2011  |   Pubmed ID: 21169444
• Examining the Global Distribution of Dominant Archaeal Populations in Soil
  The ISME Journal. May, 2011  |   Pubmed ID: 21085198
• 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
• Soil Bacterial and Fungal Communities Across a PH Gradient in an Arable Soil
  The ISME Journal. Oct, 2010  |   Pubmed ID: 20445636
• QIIME Allows Analysis of High-throughput Community Sequencing Data
  Nature Methods. May, 2010  |   Pubmed ID: 20383131
• PyNAST: a Flexible Tool for Aligning Sequences to a Template Alignment
  Bioinformatics (Oxford, England). Jan, 2010  |   Pubmed ID: 19914921
• Detecting Coevolution Without Phylogenetic Trees? Tree-ignorant Metrics of Coevolution Perform As Well As Tree-aware Metrics
  BMC Evolutionary Biology. 2008  |   Pubmed ID: 19055758
• Concept Recognition for Extracting Protein Interaction Relations from Biomedical Text
  Genome Biology. 2008  |   Pubmed ID: 18834500
• 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
• Rapid Pattern Development for Concept Recognition Systems: Application to Point Mutations
  Journal of Bioinformatics and Computational Biology. Dec, 2007  |   Pubmed ID: 18172927
• PyCogent: a Toolkit for Making Sense from Sequence
  Genome Biology. 2007  |   Pubmed ID: 17708774
• MutationFinder: a High-performance System for Extracting Point Mutation Mentions from Text
  Bioinformatics (Oxford, England). Jul, 2007  |   Pubmed ID: 17495998
• 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
• Origins of the Genetic Code: the Escaped Triplet Theory
  Annual Review of Biochemistry. 2005  |   Pubmed ID: 15952885