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J Gregory Caporaso
PeerJ Editor, Author & Reviewer
1,275 Points

Contributions by role

Author 270
Preprint Author 560
Reviewer 45
Editor 400
Comment 1
Answers 25
Links 7

Contributions by subject area

Bioinformatics
Computational Biology
Genomics
Microbiology
Ecology
Taxonomy
Ecosystem Science
Molecular Biology
Biotechnology
Human-Computer Interaction
Environmental Sciences
Data Science
Evolutionary Studies
Biodiversity
Biochemistry
Entomology
Mycology
Soil Science
Biogeochemistry

By Q&A topic

Bioinformatics
Ecology
Microbiology

J Gregory Caporaso

PeerJ Editor, Author & Reviewer

Summary

I am an Associate Professor of Biology with a focus on microbiome research and bioinformatics.

Bioinformatics Genomics Microbiology

Editorial Board Member

PeerJ - the Journal of Life & Environmental Sciences

Past or current institution affiliations

Northern Arizona University

Work details

Associate Professor

Northern Arizona University
Department of Biological Sciences

Director

Northern Arizona University
Center for Applied Microbiome Science

Websites

  • Caporaso Lab
  • GitHub
  • An Introduction to Applied Bioinforamtics
  • QIIME 2

PeerJ Contributions

  • Articles 2
  • Preprints 12
  • Edited 2
  • Answers 1
August 21, 2014
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
Jai Ram Rideout, Yan He, Jose A. Navas-Molina, William A. Walters, Luke K. Ursell, Sean M. Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C. Clemente, Jack A. Gilbert, Susan M. Huse, Hong-Wei Zhou, Rob Knight, J. Gregory Caporaso
https://doi.org/10.7717/peerj.545 PubMed 25177538
April 1, 2014
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
Jason W. Sahl, J. Gregory Caporaso, David A. Rasko, Paul Keim
https://doi.org/10.7717/peerj.332 PubMed 24749011
December 3, 2018 - Version: 2
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, II, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.27295v2
January 17, 2018 - Version: 2
Optimizing taxonomic classification of marker gene amplicon sequences
Nicholas A Bokulich, Benjamin D Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.3208v2
May 23, 2016 - Version: 1
mockrobiota: a public resource for microbiome bioinformatics benchmarking
Nicholas A Bokulich, Jai Ram Rideout, William G Mercurio, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J. Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.2065v1
February 29, 2016 - Version: 1
Geography and location are the primary drivers of office microbiome composition
John H Chase, Jennifer Fouquier, Mahnaz Zare, Derek L Sonderegger, Rob Knight, Scott Kelley, Jeffrey A Siegel, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.1797v1
January 21, 2016 - Version: 1
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Jai Ram Rideout, John H Chase, Evan Bolyen, Gail Ackermann, Antonio Gonzalez, Rob Knight, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.1670v1
October 14, 2015 - Version: 1
cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies
John H Chase, Evan T Bolyen, Jai Ram Rideout, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.1431v1
August 4, 2015 - Version: 1
Quantitative microbial ecology through stable isotope probing
Bruce A Hungate, Rebecca L Mau, Egbert Schwartz, J Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J Koch, Cindy M Liu, Theresa A McHugh, Jane C Marks, Ember M Morrissey, Lance B Price
https://doi.org/10.7287/peerj.preprints.1282v1
July 10, 2015 - Version: 2
A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
Nicholas A Bokulich, Jai Ram Rideout, Evguenia Kopylova, Evan Bolyen, Jessica Patnode, Zach Ellett, Daniel McDonald, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.934v2
May 21, 2015 - Version: 1
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Jennifer Fouquier, Jai R Rideout, Evan Bolyen, John H Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso, Scott T. Kelley
https://doi.org/10.7287/peerj.preprints.1106v1
September 22, 2014 - Version: 1
Temporal variability is a personalized feature of the human microbiome
Gilberto E Flores, J Gregory Caporaso, Jessica B Henley, Jai Ram Rideout, Daniel Domogala, John Chase, Jonathan W Leff, Yoshiki Vázquez-Baeza, Antonio Gonzalez, Rob Knight, Robert R Dunn, Noah Fierer
https://doi.org/10.7287/peerj.preprints.509v1
July 24, 2014 - Version: 2
Consistent, comprehensive and computationally efficient OTU definitions
Jai Ram Rideout, Yan He, Jose Antonio Navas-Molina, William A Walters, Luke K Ursell, Sean M Gibbons, John H Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C Clemente, Jack Gilbert, Susan M Huse, Hong-Wei Zhou, Rob Knight, J Gregory Caporaso
https://doi.org/10.7287/peerj.preprints.411v2
January 24, 2014 - Version: 1
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
Jason W Sahl, Greg Caporaso, David A Rasko, Paul S Keim
https://doi.org/10.7287/peerj.preprints.220v1

Academic Editor on

November 18, 2019
Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies
Rittik Deb, Ashwin Nair, Deepa Agashe
https://doi.org/10.7717/peerj.8058 PubMed 31763071
April 25, 2016
Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current
Martina A. Doblin, Katherina Petrou, Sutinee Sinutok, Justin R. Seymour, Lauren F. Messer, Mark V. Brown, Louiza Norman, Jason D. Everett, Allison S. McInnes, Peter J. Ralph, Peter A. Thompson, Christel S. Hassler
https://doi.org/10.7717/peerj.1973 PubMed 27168982

1 Answer

1
accepted How is taxonomy assigned to open reference OTUs?