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List of works by J Gregory Caporaso

A meta-analysis of changes in bacterial and archaeal communities with time

scientific article published on 11 April 2013

Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing

scientific article

Advancing our understanding of the human microbiome using QIIME

scientific article

Advancing the microbiome research community

scientific article

Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis

scientific article published in 2023

An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

scientific article published on 04 September 2020

An Introduction to Applied Bioinformatics: a free, open, and interactive text

scientific article published on 02 October 2018

Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort

scientific article published on 27 August 2020

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Bacterial communities associated with the lichen symbiosis

scientific article published on 17 December 2010

Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

scientific article

Best practices for analysing microbiomes

scientific article published on 01 July 2018

Cohabiting family members share microbiota with one another and with their dogs

scientific article

Collaborative cloud-enabled tools allow rapid, reproducible biological insights ⬇️

scientific article published on October 25, 2012

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

scientific article

Concept recognition for extracting protein interaction relations from biomedical text

scientific article published on September 2008

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

scientific article

Conducting a microbiome study

scientific article

Correction: The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

scientific article published on 20 December 2013

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

scientific article

Current understanding of the human microbiome.

scientific article published in April 2018

Defining seasonal marine microbial community dynamics

scientific article

Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)

scientific article published on 13 May 2020

Designing Inclusive HPV Cancer Vaccines and Increasing Uptake among Native Americans—A Cultural Perspective Review

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

scientific article

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

scientific article published on 24 April 2015

Diversity, distribution and sources of bacteria in residential kitchens

scientific article published on 22 November 2012

Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins

scientific article published on 01 April 2019

Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development

scientific article published on 16 January 2019

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

scientific article published on 31 July 2015

Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code

Evidence for a persistent microbial seed bank throughout the global ocean

scientific article (publication date: 19 March 2013)

Examining the global distribution of dominant archaeal populations in soil

scientific article published on 18 November 2010

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

scientific article published on 24 June 2021

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay

From molecules to dynamic biological communities

scientific article

Genomic Standards Consortium Projects

article

Genomic standards consortium projects

scientific article

Geography and Location Are the Primary Drivers of Office Microbiome Composition

scientific article published on March 2016

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

scientific article

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

scientific article published on 3 June 2010

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

scientific article published on 21 January 2015

Host-associated and free-living phage communities differ profoundly in phylogenetic composition

scientific article

Human gut microbiome viewed across age and geography

scientific article

Impact of Different Exercise Modalities on the Human Gut Microbiome

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

scientific article

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys ⬇️

scientific article

Individual diet has sex-dependent effects on vertebrate gut microbiota

scientific article

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

scientific article published on 22 May 2014

Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.

scientific article published on January 2008

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

scientific article published on 13 June 2016

Leptospira in river and soil in a highly endemic area of Ecuador

scientific article published on 07 January 2021

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota

scientific article published on 09 April 2019

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

scientific article

Meeting report: fungal its workshop (october 2012).

scientific article published on 15 April 2013

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

scientific article published on 23 January 2017

Microbiotyping the Sinonasal Microbiome

scientific article published on 08 April 2020

Moving pictures of the human microbiome

scientific article published in 2011

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

scientific article

Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment

scientific article published on 23 February 2022

MutationFinder: a high-performance system for extracting point mutation mentions from text

scientific article

New Insight into the Diversity of Life's Building Blocks: Evenness, Not Variance

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017

article

Open-Source Sequence Clustering Methods Improve the State Of the Art.

scientific article

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

scientific article

Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran

scientific article published on 21 November 2019

Origins of the genetic code: the escaped triplet theory.

scientific article

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?

scientific article published on 22 April 2020

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

scientific article

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

scientific article (publication date: September 2013)

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

scientific article

PyCogent: a toolkit for making sense from sequence

scientific article published in January 2007

PyNAST: a flexible tool for aligning sequences to a template alignment

scientific article (publication date: 15 January 2010)

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

scientific article published on 01 June 2020

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME allows analysis of high-throughput community sequencing data

scientific article

Qiita: rapid, web-enabled microbiome meta-analysis

scientific article published on 01 October 2018

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

scientific article

Rapid pattern development for concept recognition systems: application to point mutations

scientific article published in December 2007

Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles

scientific article published on 10 April 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Sequencing our way towards understanding global eukaryotic biodiversity

scientific article (publication date: April 2012)

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

scientific article

Soil bacterial and fungal communities across a pH gradient in an arable soil

scientific article published on 6 May 2010

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

scientific article published in November 2010

Species abundance information improves sequence taxonomy classification accuracy

scientific article published on 11 October 2019

Species-level functional profiling of metagenomes and metatranscriptomes

scholarly article by Eric A Franzosa published in October 2018

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

scientific article published on 20 May 2015

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

scientific article

Temporal variability is a personalized feature of the human microbiome

scientific article

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

2012 scientific article

The Ecology of Microbial Communities Associated with Macrocystis pyrifera

scientific article

The Western English Channel contains a persistent microbial seed bank

scientific article

The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology

scientific article published on 13 March 2020

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

scientific article published in May 2012

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

scientific article

The personal human oral microbiome obscures the effects of treatment on periodontal disease

scientific article published on 29 January 2014

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

scientific article published in July 2011

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

scientific article

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

scientific article

Using QIIME to analyze 16S rRNA gene sequences from microbial communities

article

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

scientific article published on 22 December 2015

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

scientific article published on September 2016

pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils

scholarly article by Youzhi Feng et al published July 2014 in Soil Biology and Biochemistry

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

scientific article published on 20 November 2018

q2-sample-classifier: machine-learning tools for microbiome classification and regression

scientific article published on 23 October 2018

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