Editorial: Genomics and metagenomics approaches for food value chain quality, safety, and product development

by Barretto, Caroline, Combrisson, Jerome, Bokulich, Nicholas; id_orcid0000-0002-1784-8935
Published 2022

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

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Dillon, Matthew R., Bolyen, Evan, Kaehler, Benjamin D., Huttley, Gavin A., Caporaso, J. Gregory
Published 2018

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

by Kaehler, Benjamin D., Bokulich, Nicholas; id_orcid0000-0002-1784-8935, McDonald, Daniel, Knight, Rob, Caporaso, J. Gregory, Huttley, Gavin A.
Published 2019

Revisiting microbe-metabolite interactions: doing better than random

by Morton, James T., McDonald, Daniel, Aksenov, Alexander A., Nothias, Louis Felix, Foulds, James R., Quinn, Robert A., Badri, Michelle H., Swenson, Tami L., Van Goethem, Marc W., Northen, Trent R., Vázquez-Baeza, Yoshiki, Wang, Mingxun, Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Watters, Aaron, Song, Se Jin, Bonneau, Richard, Dorrestein, Pieter C., Knight, Rob
Published 2019

Species abundance information improves sequence taxonomy classification accuracy

by Kaehler, Benjamin D., Bokulich, Nicholas; id_orcid0000-0002-1784-8935, McDonald, Daniel, Knight, Rob, Caporaso, J. Gregory, Huttley, Gavin A.
Published 2019

Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Ziemski, Michal; id_orcid0000-0001-6285-8852, Robeson II, Michael S., Kaehler, Benjamin D.
Published 2020

Next-generation approaches to the microbial ecology of food fermentations

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Mills, David A.
Published 2012

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences

by Ziemski, Michal; id_orcid0000-0001-6285-8852, Wisanwanichthan, Treepop, Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Kaehler, Benjamin D.
Published 2021

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Bergsveinson, Jordyn, Ziola, Barry, Mills, David A.
Published 2015

Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Maldonado, Juan, Kang, Dae-Wook, Krajmalnik-Brown, Rosa, Caporaso, J. Gregory
Published 2019

Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Collins, Thomas S., Masarweh, Chad, Allen, Greg, Heymann, Hildegarde, Ebeler, Susan E., Mills, David A.
Published 2016

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Bamforth, Charles W., Mills, David A.
Published 2012

mockrobiota: a public resource for microbiome bioinformatics benchmarking

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Rideout, Jai Ram, Mercurio, William G., Shiffer, Arron, Wolfe, Benjamin, Maurice, Corinne F., Dutton, Rachel J., Turnbaugh, Peter J., Knight, Rob, Caporaso, J. Gregory
Published 2016

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

by Nobel, Yael R., Cox, Laura M., Kirigin, Francis F., Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Yamanishi, Shingo, Teitler, Isabel, Chung, Jennifer, Sohn, Jiho, Barber, Cecily M., Goldfarb, David S., Raju, Kartik, Abubucker, Sahar, Zhou, Yanjiao, Ruiz, Victoria E., Li, Huilin, Mitreva, Makedonka, Alekseyenko, Alexander V., Weinstock, George M., Sodergren, Erica, Blaser, Martin J.
Published 2015

Monitoring seasonal changes in winery-resident microbiota

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Ohta, Moe, Richardson, Paul M., Mills, David A.
Published 2013

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

by Kaplan, Ian, Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Caporaso, J. Gregory, Enders, Laramy S., Ghanem, Wadih, Ingerslew, Kathryn S.
Published 2020

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

by Ladner, Jason T., Larsen, Brendan B., Bowers, Jolene R., Hepp, Crystal M., Bolyen, Evan, Folkerts, Megan, Sheridan, Krystal, Pfeiffer, Ashlyn, Yaglom, Hayley, Lemmer, Darrin, Sahl, Jason W., Kaelin, Emily A., Maqsood, Rabia, Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Quirk, Grace, Watts, Thomas D., Komatsu, Kenneth, Waddell, Victor, Lim, Efrem S., Caporaso, J. Gregory, Engelthaler, David M., Worobey, Michael, Keim, Paul
Published 2020

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

by Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Dillon, Matthew R., Zhang, Yilong, Rideout, Jai Ram, Bolyen, Evan, Li, Huilin, Albert, Paul S., Caporaso, J. Gregory
Published 2018

Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice

by Ma, Betty W., Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Castillo, Patricia A., Kananurak, Anchasa, Underwood, Mark A., Mills, David A., Bevins, Charles L
Published 2012

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

by Mahana, Douglas, Trent, Chad M., Kurtz, Zachary D., Bokulich, Nicholas; id_orcid0000-0002-1784-8935, Battaglia, Thomas, Chung, Jennifer, Müller, Christian L., Li, Huilin, Bonneau, Richard A., Blaser, Martin J.
Published 2016