E. Bolyen

发表

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.

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

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

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..

Optimizing taxonomic classification of marker gene sequences

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

short-read-tax-assignment: Paper revision release

Evan Bolyen, Jai Ram Rideout, Greg Caporaso, 2015 .

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

Rob Knight, Gavin A. Huttley, J. Gregory Caporaso, 2018, Microbiome.

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

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

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

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

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

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

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

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

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.

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.

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

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

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

P. Keim, V. Waddell, D. Engelthaler, 2020, medRxiv.

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.

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.

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 .

Predicting Neurodegenerative Disease Using Prepathology Gut Microbiota Composition: a Longitudinal Study in Mice Modeling Alzheimer’s Disease Pathologies

Emily K. Cope, Christopher R. Keefe, J. Caporaso, 2023, Microbiology spectrum.

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

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

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.

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.

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

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

PepSIRF + QIIME 2: software tools for automated, reproducible analysis of highly-multiplexed serology data

J. Ladner, E. Bolyen, J. Altin, 2022, 2207.11509.

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

Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, 2018, The Journal of open source education.

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

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