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ArticlesPeer ReviewedFull Text
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Author / Creator:Bokulich, Nicholas A. ; Kaehler, Benjamin D. ; Rideout, Jai Ram ; Dillon, Matthew ; Bolyen, Evan ; Knight, Rob ; Huttley, Gavin A. ; Gregory Caporaso, J.
Publisher:England: BioMed Central Ltd
Journal title:Microbiome, 2018-05, Vol.6 (1), p.90-90, Article 90
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q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
Author / Creator:Bokulich, Nicholas A. ; Dillon, Matthew R. ; Zhang, Yilong ; Rideout, Jai Ram ; Bolyen, Evan ; Li, Huilin ; Albert, Paul S. ; Caporaso, J. Gregory
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2018-11, Vol.3 (6)
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Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay
Author / Creator:Keefe, Christopher R. ; Dillon, Matthew R. ; Gehret, Elizabeth ; Herman, Chloe ; Jewell, Mary ; Wood, Colin V. ; Bolyen, Evan ; Caporaso, J. Gregory
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2023-11, Vol.19 (11), p.e1011676-e1011676
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Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots [version 1; peer review: awaiting peer review]
Author / Creator:Raspet, Isaiah ; Gehret, Elizabeth ; Herman, Chloe ; Meilander, Jeff ; Manley, Andrew ; Simard, Anthony ; Bolyen, Evan ; Caporaso, J Gregory
Publisher:F1000 Research Ltd
Journal title:F1000 research, 2025, Vol.14, p.87
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Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity [version 2; peer review: 2 approved]
Author / Creator:Bolyen, Evan ; Dillon, Matthew R ; Bokulich, Nicholas A ; Ladner, Jason T ; Larsen, Brendan B ; Hepp, Crystal M ; Lemmer, Darrin ; Sahl, Jason W ; Sanchez, Andrew ; Holdgraf, Chris ; Sewell, Chris ; Choudhury, Aakash G ; Stachurski, John ; McKay, Matthew ; Simard, Anthony ; Engelthaler, David M ; Worobey, Michael ; Keim, Paul ; Caporaso, J. Gregory
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2020, Vol.9, p.657-657
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Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Author / Creator:Rideout, Jai Ram ; Chase, John H ; Bolyen, Evan ; Ackermann, Gail ; González, Antonio ; Knight, Rob ; Caporaso, J Gregory
Publisher:United States: Oxford University Press
Journal title:Gigascience, 2016-06, Vol.5 (1), p.27-27, Article 27
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cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
Author / Creator:Chase, John H. ; Bolyen, Evan ; Rideout, Jai Ram ; Caporaso, J. Gregory
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2016-01, Vol.1 (1)
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ArticlesPeer ReviewedFull Text
q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
Author / Creator:Bokulich, Nicholas A. ; Dillon, Matthew R. ; Zhang, Yilong ; Rideout, Jai Ram ; Bolyen, Evan ; Li, Huilin ; Albert, Paul S. ; Caporaso, J. Gregory
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2018-11, Vol.3 (6)
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Qiita: rapid, web-enabled microbiome meta-analysis
Author / Creator:Gonzalez, Antonio ; Navas-Molina, Jose A. ; Kosciolek, Tomasz ; McDonald, Daniel ; Vázquez-Baeza, Yoshiki ; Ackermann, Gail ; DeReus, Jeff ; Janssen, Stefan ; Swafford, Austin D. ; Orchanian, Stephanie B. ; Sanders, Jon G. ; Shorenstein, Joshua ; Holste, Hannes ; Petrus, Semar ; Robbins-Pianka, Adam ; Brislawn, Colin J. ; Wang, Mingxun ; Rideout, Jai Ram ; Bolyen, Evan ; Dillon, Matthew ; Caporaso, J. Gregory ; Dorrestein, Pieter C. ; Knight, Rob
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2018-10, Vol.15 (10), p.796-798
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ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Author / Creator:Fouquier, Jennifer ; Rideout, Jai Ram ; Bolyen, Evan ; Chase, John ; Shiffer, Arron ; McDonald, Daniel ; Knight, Rob ; Caporaso, J Gregory ; Kelley, Scott T.
Publisher:England: BioMed Central Ltd
Journal title:Microbiome, 2016-02, Vol.4 (1), p.11-11, Article 11
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Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops
Author / Creator:Dillon, Matthew R. ; Bolyen, Evan ; Adamov, Anja ; Belk, Aeriel ; Borsom, Emily ; Burcham, Zachary ; Debelius, Justine W. ; Deel, Heather ; Emmons, Alex ; Estaki, Mehrbod ; Herman, Chloe ; Keefe, Christopher R. ; Morton, Jamie T. ; Oliveira, Renato R. M. ; Sanchez, Andrew ; Simard, Anthony ; Vázquez-Baeza, Yoshiki ; Ziemski, Michal ; Miwa, Hazuki E. ; Kerere, Terry A. ; Coote, Carline ; Bonneau, Richard ; Knight, Rob ; Oliveira, Guilherme ; Gopalasingam, Piraveen ; Kaehler, Benjamin D. ; Cope, Emily K. ; Metcalf, Jessica L. ; Robeson II, Michael S. ; Bokulich, Nicholas A. ; Caporaso, J. Gregory
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-06, Vol.17 (6), p.e1009056
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ArticlesPeer ReviewedFull Text
q2-sample-classifier: machine-learning tools for microbiome classification and regression
Author / Creator:Bokulich, Nicholas A ; Dillon, Matthew R ; Bolyen, Evan ; Kaehler, Benjamin D ; Huttley, Gavin A ; Caporaso, J Gregory
Publisher:England
Journal title:Journal of open research software, 2018, Vol.3 (30)
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ArticlesPeer ReviewedFull Text
Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity [version 1; peer review: 1 approved, 1 approved with reservations]
Author / Creator:Bolyen, Evan ; Dillon, Matthew R ; Bokulich, Nicholas A ; Ladner, Jason T ; Larsen, Brendan B ; Hepp, Crystal M ; Lemmer, Darrin ; Sahl, Jason W ; Sanchez, Andrew ; Holdgraf, Chris ; Sewell, Chris ; Choudhury, Aakash G ; Stachurski, John ; McKay, Matthew ; Engelthaler, David M ; Worobey, Michael ; Keim, Paul ; Caporaso, J. Gregory
Journal title:F1000 research, 2020, Vol.9, p.657
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ArticlesFull Text
Optimizing taxonomic classification of marker gene sequences
Author / Creator:Bokulich, Nicholas A ; Kaehler, Benjamin D ; Jai Ram Rideout ; Dillon, Matthew ; Bolyen, Evan ; Knight, Rob ; Huttley, Gavin A ; Caporaso, J Gregory
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2017-08
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ArticlesFull Text
cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies
Author / Creator:Chase, John H ; Bolyen, Evan T ; Jai Ram Rideout ; Caporaso, J Gregory
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2015-10
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ArticlesFull Text
Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Author / Creator:Jai Ram Rideout ; Chase, John H ; Bolyen, Evan ; Ackermann, Gail ; Gonzalez, Antonio ; Knight, Rob ; Caporaso, J Gregory
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2016-01
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ArticlesFull Text
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Author / Creator:Fouquier, Jennifer ; Rideout, Jai R ; Bolyen, Evan ; Chase, John H ; Shiffer, Arron ; McDonald, Daniel ; Knight, Rob ; Caporaso, J Gregory ; Kelley, Scott T
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2015-05
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A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
Author / Creator:Bokulich, Nicholas A ; Jai Ram Rideout ; Kopylova, Evguenia ; Bolyen, Evan ; Patnode, Jessica ; Ellett, Zach ; McDonald, Daniel ; Wolfe, Benjamin ; Maurice, Corinne F ; Dutton, Rachel J ; Turnbaugh, Peter J ; Knight, Rob ; Caporaso, J Gregory
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2015-07
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MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework
Author / Creator:Ziemski, Michal ; Gehret, Liz ; Simard, Anthony ; Santiago Castro Dau ; Risch, Vinzent ; Grabocka, Doriela ; Matzoros, Christos ; Wood, Colin ; Paula Momo Cabrera ; Hernandez-Velazquez, Rodrigo ; Herman, Chloe ; Evans, Keegan ; Robeson, Michael S ; Bolyen, Evan ; Caporaso, J Gregory ; Bokulich, Nicholas A
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2025-01
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Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt
Author / Creator:Herman, Chloe ; Bolyen, Evan ; Simard, Anthony ; Gehret, Liz ; Caporaso, J Gregory
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2024-11
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Showing 1 to 20 of 26 results

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

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

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Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay

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Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots [version 1; peer review: awaiting peer review]

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Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity [version 2; peer review: 2 approved]

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

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

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

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Qiita: rapid, web-enabled microbiome meta-analysis

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

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

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

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Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity [version 1; peer review: 1 approved, 1 approved with reservations]

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Optimizing taxonomic classification of marker gene sequences

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cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies

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

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

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

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MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

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Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt

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