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

by Huttley Gavin A, Hunter Lawrence, Easton Brett C, Smit Sandra, Caporaso J Gregory, Knight Rob
Published 2008-12-01

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

by He, Yan, Caporaso, J Gregory, Jiang, Xiao-Tao, Sheng, Hua-Fang, Huse, Susan M, Rideout, Jai Ram, Edgar, Robert C, Kopylova, Evguenia, Walters, William A, Knight, Rob, Zhou, Hong-Wei
Published 2015

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

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

by Pirrung, Meg, Kennedy, Ryan, Caporaso, J Gregory, Stombaugh, Jesse, Wendel, Doug, Knight, Rob
Published 2011

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

Species abundance information improves sequence taxonomy classification accuracy.

by Kaehler, Benjamin D, Bokulich, Nicholas A, McDonald, Daniel, Knight, Rob, Caporaso, J Gregory, Huttley, Gavin A
Published 2019

Host-associated and free-living phage communities differ profoundly in phylogenetic composition.

by Caporaso, J Gregory, Knight, Rob, Kelley, Scott T
Published 2011

PyCogent: a toolkit for making sense from sequence.

by Knight, Rob, Maxwell, Peter, Birmingham, Amanda, Carnes, Jason, Caporaso, J Gregory, Easton, Brett C, Eaton, Michael, Hamady, Micah, Lindsay, Helen, Liu, Zongzhi, Lozupone, Catherine, McDonald, Daniel, Robeson, Michael, Sammut, Raymond, Smit, Sandra, Wakefield, Matthew J, Widmann, Jeremy, Wikman, Shandy, Wilson, Stephanie, Ying, Hua, Huttley, Gavin A
Published 2007

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

by Caporaso, J Gregory, Lauber, Christian L, Walters, William A, Berg-Lyons, Donna, Huntley, James, Fierer, Noah, Owens, Sarah M, Betley, Jason, Fraser, Louise, Bauer, Markus, Gormley, Niall, Gilbert, Jack A, Smith, Geoff, Knight, Rob
Published 2012

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

by Langille, Morgan GI, Zaneveld, Jesse, Caporaso, J Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A, Clemente, Jose C, Burkepile, Deron E, Vega Thurber, Rebecca L, Knight, Rob, Beiko, Robert G, Huttenhower, Curtis
Published 2013

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

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

by Bolnick, Daniel I, Snowberg, Lisa K, Hirsch, Philipp E, Lauber, Christian L, Knight, Rob, Caporaso, J Gregory, Svanbäck, Richard
Published 2014

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

by McDonald, Daniel, Clemente, Jose C, Kuczynski, Justin, Rideout, Jai Ram, Stombaugh, Jesse, Wendel, Doug, Wilke, Andreas, Huse, Susan, Hufnagle, John, Meyer, Folker, Knight, Rob, Caporaso, J Gregory
Published 2012

Species-level functional profiling of metagenomes and metatranscriptomes.

by Franzosa, Eric A, McIver, Lauren J, Rahnavard, Gholamali, Thompson, Luke R, Schirmer, Melanie, Weingart, George, Lipson, Karen Schwarzberg, Knight, Rob, Caporaso, J Gregory, Segata, Nicola, Huttenhower, Curtis
Published 2018

The Western English Channel contains a persistent microbial seed bank.

by Caporaso, J Gregory, Paszkiewicz, Konrad, Field, Dawn, Knight, Rob, Gilbert, Jack A
Published 2012

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

by Sinha, Rashmi, Ahsan, Habibul, Blaser, Martin, Caporaso, J Gregory, Carmical, Joseph Russell, Chan, Andrew T, Fodor, Anthony, Gail, Mitchell H, Harris, Curtis C, Helzlsouer, Kathy, Huttenhower, Curtis, Knight, Rob, Kong, Heidi H, Lai, Gabriel Y, Hutchinson, Diane Leigh Smith, Le Marchand, Loic, Li, Hongzhe, Orlich, Michael J, Shi, Jianxin, Truelove, Ann, Verma, Mukesh, Vogtmann, Emily, White, Owen, Willett, Walter, Zheng, Wei, Mahabir, Somdat, Abnet, Christian
Published 2018

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

by Bokulich, Nicholas A, 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

Individual diet has sex-dependent effects on vertebrate gut microbiota.

by Bolnick, Daniel I, Snowberg, Lisa K, Hirsch, Philipp E, Lauber, Christian L, Org, Elin, Org, Elin, Parks, Brian, Lusis, Aldons J, Knight, Rob, Caporaso, J Gregory, Svanbäck, Richard
Published 2014

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

Human gut microbiome viewed across age and geography.

by Yatsunenko, Tanya, Rey, Federico E, Manary, Mark J, Trehan, Indi, Dominguez-Bello, Maria Gloria, Contreras, Monica, Magris, Magda, Hidalgo, Glida, Baldassano, Robert N, Anokhin, Andrey P, Heath, Andrew C, Warner, Barbara, Reeder, Jens, Kuczynski, Justin, Caporaso, J Gregory, Lozupone, Catherine A, Lauber, Christian, Clemente, Jose Carlos, Knights, Dan, Knight, Rob, Gordon, Jeffrey I
Published 2012