J. Caporaso

发表

Concept recognition for extracting protein interaction relations from biomedical text

Helen L. Johnson, Elizabeth K. White, Olga Medvedeva, 2008, Genome Biology.

Moving pictures of the human microbiome

R. Knight, P. Gajer, J. Ravel, 2011, Genome Biology.

The Western English Channel contains a persistent microbial seed bank

R. Knight, J. Gilbert, J. Caporaso, 2011, The ISME Journal.

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

William A. Walters, R. Knight, J. Caporaso, 2010, Proceedings of the National Academy of Sciences.

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

Rob Knight, Noah Fierer, Paul Grogan, 2010, Environmental microbiology.

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

R. Knight, J. Caporaso, N. Fierer, 2010, The ISME Journal.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nicholas A. Bokulich, D. Gevers, R. Knight, 2012, Nature Methods.

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

William A. Walters, J. Betley, R. Knight, 2012, The ISME Journal.

Best practices for analysing microbiomes

Luke R. Thompson, James T. Morton, Justine W. Debelius, 2018, Nature Reviews Microbiology.

Soluble corn fiber reduces ovalbumin-induced sinonasal inflammation via the gut microbiota-airway axis

Nicholas A. Bokulich, Emily K. Cope, J. Caporaso, 2020, bioRxiv.

Species abundance information improves sequence taxonomy classification accuracy

Benjamin D. Kaehler, Nicholas A. Bokulich, R. Knight, 2019, Nature Communications.

Optimizing taxonomic classification of marker gene 1 sequences 2 3

Benjamin D. Kaehler, Nicholas A. Bokulich, Matthew R. Dillon, 2017 .

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

Nicholas A. Bokulich, R. Knight, J. Caporaso, 2016, mSystems.

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

Se Jin Song, J. Clemente, R. Knight, 2013, eLife.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018

Daniel J. Nasko, Daniel D. Sommer, Brian D. Ondov, 2018, Microbiome.

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

William A. Walters, Robert C. Edgar, R. Edgar, 2015, Microbiome.

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

Jesse R. Zaneveld, C. Huttenhower, J. Clemente, 2013, Nature Biotechnology.

Species-level functional profiling of metagenomes and metatranscriptomes

Luke R. Thompson, C. Huttenhower, N. Segata, 2018, Nature Methods.

Individual diet has sex-dependent effects on vertebrate gut microbiota

R. Knight, J. Caporaso, C. Lauber, 2014, Nature Communications.

Sequencing our way towards understanding global eukaryotic biodiversity.

R. Knight, W. Thomas, J. Caporaso, 2012, Trends in ecology & evolution.

Origins of the genetic code: the escaped triplet theory.

R. Knight, J. Caporaso, M. Yarus, 2005, Annual review of biochemistry.

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

Scott T. Bates, J. Gilbert, J. Caporaso, 2012, Proceedings of the National Academy of Sciences.

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

William A. Walters, L. T. Angenent, R. Knight, 2011, The ISME Journal.

The under-recognized dominance of Verrucomicrobia in soil bacterial communities.

Scott T. Bates, R. Knight, J. Caporaso, 2011, Soil biology & biochemistry.

Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities

William A. Walters, R. Knight, J. Caporaso, 2012, Current protocols in microbiology.

Conducting a Microbiome Study

William A. Walters, Angela C. Poole, R. Knight, 2014, Cell.

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

William A. Walters, R. Knight, J. Gilbert, 2015, mSystems.

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

Rob Knight, Gavin A Huttley, J Gregory Caporaso, 2008, BMC Evolutionary Biology.

Advancing our understanding of the human microbiome using QIIME.

Rob Knight, Donna Berg-Lyons, James Huntley, 2013, Methods in enzymology.

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

J. Gregory Caporaso, Paul Keim, Jason W. Sahl, 2014, PeerJ.

Diversity, distribution and sources of bacteria in residential kitchens.

Rob Knight, Noah Fierer, J Gregory Caporaso, 2013, Environmental microbiology.

Temporal variability is a personalized feature of the human microbiome

Rob Knight, Antonio Gonzalez, Noah Fierer, 2014, Genome Biology.

Current understanding of the human microbiome

Rob Knight, J Gregory Caporaso, Martin J Blaser, 2018, Nature Medicine.

The international sinonasal microbiome study (ISMS): a multi-centre, multi-national collaboration characterising the microbial ecology of the sinonasal cavity

Matthew R. Dillon, Emily K. Cope, J. Caporaso, 2019, bioRxiv.

The international sinonasal microbiome study (ISMS): a multi-centre, international characterization of sinonasal bacterial ecology

Matthew R. Dillon, Emily K. Cope, J. Caporaso, 2019 .

Evidence for a persistent microbial seed bank throughout the global ocean

R. Knight, J. Gilbert, J. Caporaso, 2013, Proceedings of the National Academy of Sciences.

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

D. Gevers, J. Clemente, L. Ursell, 2012, The Journal of allergy and clinical immunology.

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

R. Knight, J. Caporaso, S. Kelley, 2011, PloS one.

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

Rob Knight, J Gregory Caporaso, Largus T Angenent, 2011, The ISME Journal.

From molecules to dynamic biological communities

William A. Walters, R. Knight, J. Caporaso, 2013, Biology & Philosophy.

A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments

Rob Knight, Daniel McDonald, J. Gregory Caporaso, 2015 .

Geography and location are the primary drivers

John H. Chase, R. Knight, J. Caporaso, 2016 .

Quantitative Microbial Ecology through Stable Isotope Probing

J. Caporaso, L. Price, B. Hungate, 2015, Applied and Environmental Microbiology.

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

J. Caporaso, V. Waddell, T. Watts, 2020, mBio.

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

Christopher R Keefe, Benjamin D. Kaehler, Nicholas A. Bokulich, 2021, PLoS Comput. Biol..

Consistent, comprehensive and computationally efficient OTU definitions

William A. Walters, Jose A Navas-Molina, Susan M. Huse, 2014 .

Contribute to Temporal Changes in Microbial Diversity Conditionally Rare Taxa Disproportionately 2014

R. Knight, J. Gilbert, J. Handelsman, 2014 .

Optimizing taxonomic classification of marker gene sequences

Benjamin D. Kaehler, Matthew R. Dillon, R. Knight, 2017 .

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

William A. Walters, R. Edgar, R. Knight, 2015, Microbiome.

Geography and Location Are the Primary Drivers of Office Microbiome Composition

John H. Chase, R. Knight, J. Caporaso, 2016, mSystems.

Author response: Cohabiting family members share microbiota with one another and with their dogs

Se Jin Song, J. Clemente, R. Knight, 2013 .

Defining seasonal marine microbial community dynamics

R. Knight, J. Gilbert, J. Caporaso, 2011, The ISME Journal.

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)

Rob Knight, Antonio Gonzalez, J. Gregory Caporaso, 2013, PloS one.

Microbiotyping the Sinonasal Microbiome

Matthew R. Dillon, Emily K. Cope, J. Caporaso, 2019, bioRxiv.

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

Fiona Ginty, Mark P. Styczynski, Ilya Shmulevich, 2020, Trends in cancer.

of Nebraska - Lincoln Advancing the Microbiome Research Community Advancing the Microbiome Research Community

C. Huttenhower, E. Franzosa, D. Gevers, 2020 .

Ecology of microbial communities

R. Knight, J. Caporaso, S. Palumbi, 1988 .

Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey.

E. Vogtmann, X. Hua, Jianxin Shi, 2022, The Lancet. Microbe.

A communal catalogue reveals Earth’s multiscale microbial diversity

Rick L. Stevens, William A. Walters, Nicole M. Gaudelli, 2017, Nature.

Bacterial Communities Associated with the Lichen Symbiosis

Scott T. Bates, R. Knight, J. Caporaso, 2010, Applied and Environmental Microbiology.

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

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Changes in the taxonomic / phylogenetic composition of fecal communities as a function of age and population

J. Clemente, R. Knight, J. Caporaso, 2016 .

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

Rob Knight, J. Gregory Caporaso, Kyle Bittinger, 2009, Bioinform..

Phylogenetic organization of bacterial activity

J. Caporaso, L. Price, B. Hungate, 2016, The ISME Journal.

Defining seasonal marine microbial community dynamics

Susan M. Huse, R. Knight, J. Gilbert, 2011, The ISME Journal.

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

William A. Walters, Ahmad Turan Naimey, Lasse Buur Rasmussen, 2019, Nature Biotechnology.

Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities

Rob Knight, William A. Walters, Jesse Stombaugh, 2011, Current protocols in bioinformatics.

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

Francesco Asnicar, Mingxun Wang, Pieter C. Dorrestein, 2018 .

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

D. Post, R. Knight, J. Caporaso, 2014, Ecology letters.

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

Gavin A. Huttley, J. Gregory Caporaso, Evan Bolyen, 2018, bioRxiv.

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

John H. Chase, R. Knight, J. Caporaso, 2016, Microbiome.

Qiita: rapid, web-enabled microbiome meta-analysis

Mingxun Wang, Rob Knight, Evan Bolyen, 2018, Nature Methods.

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

Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, 2011, Bioinform..

Environmental Exposures Influence Nasal Microbiome Composition in a Longitudinal Study of Division I Collegiate Athletes

R. A. Johns, Emily K. Cope, J. Caporaso, 2020, bioRxiv.

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

Matthew R. Dillon, Emily K. Cope, J. Caporaso, 2020, Allergy.

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

Rob Knight, J. Gregory Caporaso, Frédéric Mahé, 2016, mSystems.

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

J. Gregory Caporaso, Evan Bolyen, Jai Ram Rideout, 2015, mSystems.

The Human Microbiome: Getting Personal Eachofusharborsauniquemicrobiome,anditscharacteristicsplayanimportant roleindifferentiatingusfromoneanother

R. Knight, J. Caporaso, Antonio Gonzalez, 2014 .

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

Antonio Gonzalez, Jack A. Gilbert, Yan He, 2014, PeerJ.

The Human Microbiome: Getting Personal Eachofusharborsauniquemicrobiome,anditscharacteristicsplayanimportant roleindifferentiatingusfromoneanother

R. Knight, J. Caporaso, Antonio Gonzalez, 2014 .

Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks

K. Bretonnel Cohen, Lawrence Hunter, Philip E. Bourne, 2007, Pacific Symposium on Biocomputing.

Advancing the Microbiome Research Community

Rob Knight, Dan Knights, J. Gregory Caporaso, 2014, Cell.

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering

Zhiyong Lu, K. Bretonnel Cohen, Helen L. Johnson, 2006, TREC.

Examining the global distribution of dominant archaeal populations in soil

Rob Knight, Donna Berg-Lyons, Noah Fierer, 2011, The ISME Journal.

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

William E. Stutz, R. Knight, J. Caporaso, 2014, Molecular ecology.

Best practices for analysing microbiomes

Luke R. Thompson, James T. Morton, Justine W. Debelius, 2018, Nature Reviews Microbiology.

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

Emily K. Cope, J. Caporaso, P. Keim, 2019, Anaerobe.

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity.

Michael Worobey, Chris Holdgraf, J. Gregory Caporaso, 2020, F1000Research.

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

Huilin Li, Paul S Albert, Evan Bolyen, 2018, mSystems.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

J. Caporaso, M. Seeger, S. Fuentes, 2015, Applied and Environmental Microbiology.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

Jo Handelsman, Rob Knight, Jack A. Gilbert, 2014, mBio.

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

J. Caporaso, T. Thomas, A. Campbell, 2015, Environmental microbiology.

Qiita: rapid, web-enabled microbiome meta-analysis

Colin J. Brislawn, Matthew R. Dillon, Jose A. Navas-Molina, 2018, Nature Methods.

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

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

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

R. Knight, J. Caporaso, Youzhi Feng, 2014 .

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

William W. Van Treuren, R. Knight, J. Gilbert, 2017, mSystems.

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

William A. Walters, N. Lennon, J. Caporaso, 2016, Applied and Environmental Microbiology.

Title Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2 ' s q 2-feature-classifier plugin Permalink

Benjamin D. Kaehler, Nicholas A. Bokulich, Matthew R. Dillon, 2018 .

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

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2007, Bioinform..

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

C. Huttenhower, H. Kong, E. Vogtmann, 2018, Microbiome.

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms

J. Gilbert, J. Caporaso, S. Gibbons, 2012 .

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

Matthew R. Dillon, J. Stachurski, J. Caporaso, 2020, F1000Research.

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

Pieter C. Dorrestein, J. Gregory Caporaso, Sean M. Gibbons, 2017, mSystems.

Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location

V. Fofanov, J. Caporaso, P. Keim, 2020, bioRxiv.

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

Rob Knight, Qiyun Zhu, Evan Bolyen, 2020, Current protocols in bioinformatics.

Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments

L. Ursell, R. Knight, J. Caporaso, 2015 .

A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples.

J. Caporaso, M. Rothrock, K. Hiett, 2014, Journal of visualized experiments : JoVE.

Meeting Report: Fungal ITS Workshop (October 2012)

Rob Knight, Laura Wegener Parfrey, Daniel McDonald, 2013, Standards in genomic sciences.

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

Rob Knight, J. Gregory Caporaso, Evan Bolyen, 2016, GigaScience.

The Ecology of Microbial Communities Associated with Macrocystis pyrifera

R. Knight, J. Caporaso, S. Palumbi, 2013, PloS one.

Species-level microbial sequence classification is improved by source-environment information

Gavin A. Huttley, J. Gregory Caporaso, Benjamin D. Kaehler, 2018, bioRxiv.

Species-level functional profiling of metagenomes and metatranscriptomes

Luke R. Thompson, C. Huttenhower, N. Segata, 2018, Nature Methods.

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

William A. Walters, Susan M. Huse, Robert C. Edgar, 2015, Microbiome.

From molecules to dynamic biological communities

William A. Walters, R. Knight, J. Caporaso, 2013, Biology & philosophy.

A Comparison of the Small-Sample Properties of Several Estimators for Spatial-Lag Count Models

David S. Siroky, John H. Freeman, Jonathan N. Katz, 2009 .

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

Rob Knight, J. Gregory Caporaso, Jesse Stombaugh, 2011, Bioinform..

Correction: The Ecology of Microbial Communities Associated with Macrocystis pyrifera

R. Knight, J. Caporaso, S. Palumbi, 2013, PLoS ONE.

Daniel J. Nasko, Daniel D. Sommer, Brian D. Ondov, 2018, Microbiome.

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

W. Willett, C. Huttenhower, H. Kong, 2018, Microbiome.

Evaluation of software impact designed for biomedical research: Are we measuring what’s meaningful?

Cambridge, Northern Arizona University, Seattle, 2023, ArXiv.

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

Benjamin D. Kaehler, Nicholas A. Bokulich, Matthew R. Dillon, 2018, Microbiome.

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

R. Knight, N. Pace, H. Tufo, 2012, The ISME Journal.

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

Benjamin D. Kaehler, Nicholas A. Bokulich, Matthew R. Dillon, 2018, bioRxiv.

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

J. Caporaso, M. Yarus, R. Knight, 2005, Journal of Molecular Evolution.

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2007, J. Bioinform. Comput. Biol..

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

J. Caporaso, N. Fierer, C. Lauber, 2010, The ISME Journal.

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

John H. Chase, J. Caporaso, S. Kelley, 2016, Microbiome.

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

L. T. Angenent, J. Caporaso, R. Ley, 2011, The ISME Journal.

The international sinonasal microbiome study (ISMS): a multi- 1 centre, international characterization of sinonasal bacterial ecology 2

Matthew R. Dillon, J. Caporaso, A. Shiffer, 2019 .

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

Nicholas A. Bokulich, Matthew R. Dillon, J. Caporaso, 2018, mSystems.

Temporal variability is a personalized feature of the human microbiome

John H. Chase, J. Caporaso, N. Fierer, 2014, Genome Biology.

Additional file 7

John H. Chase, J. Caporaso, N. Fierer, 2010 .

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

Susan M. Huse, J. Caporaso, Evguenia Kopylova, 2015, Microbiome.

q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data

Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, 2017, bioRxiv.