EMPeror: a tool for visualizing high-throughput microbial community data

por Vázquez-Baeza, Yoshiki, Pirrung, Meg, Gonzalez, Antonio, Knight, Rob
Publicado 2013

From molecules to dynamic biological communities

por McDonald, Daniel, Vázquez-Baeza, Yoshiki, Walters, William A., Caporaso, J. Gregory, Knight, Rob
Publicado 2013

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project

por Debelius, Justine W., Vázquez-Baeza, Yoshiki, McDonald, Daniel, Xu, Zhenjiang, Wolfe, Elaine, Knight, Rob
Publicado 2016

Tiny microbes, enormous impacts: what matters in gut microbiome studies?

por Debelius, Justine, Song, Se Jin, Vazquez-Baeza, Yoshiki, Xu, Zhenjiang Zech, Gonzalez, Antonio, Knight, Rob
Publicado 2016

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data

por Armstrong, George, Martino, Cameron, Rahman, Gibraan, Gonzalez, Antonio, Vázquez-Baeza, Yoshiki, Mishne, Gal, Knight, Rob
Publicado 2021

Guiding longitudinal sampling in IBD cohorts

por Vázquez-Baeza, Yoshiki, Gonzalez, Antonio, Xu, Zhenjiang Zech, Washburne, Alex, Herfarth, Hans H, Sartor, R Balfour, Knight, Rob
Publicado 2018

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

por Mills, Robert H., Vázquez-Baeza, Yoshiki, Zhu, Qiyun, Jiang, Lingjing, Gaffney, James, Humphrey, Greg, Smarr, Larry, Knight, Rob, Gonzalez, David J.
Publicado 2019

Meta-analyses of studies of the human microbiota

por Lozupone, Catherine A., Stombaugh, Jesse, Gonzalez, Antonio, Ackermann, Gail, Wendel, Doug, Vázquez-Baeza, Yoshiki, Jansson, Janet K., Gordon, Jeffrey I., Knight, Rob
Publicado 2013

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

por Jiang, Lingjing, Haiminen, Niina, Carrieri, Anna‐Paola, Huang, Shi, Vázquez‐Baeza, Yoshiki, Parida, Laxmi, Kim, Ho‐Cheol, Swafford, Austin D., Knight, Rob, Natarajan, Loki
Publicado 2021

Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases

por Rahman, Gibraan, McDonald, Daniel, Gonzalez, Antonio, Vázquez-Baeza, Yoshiki, Jiang, Lingjing, Casals-Pascual, Climent, Hakim, Daniel, Dilmore, Amanda Hazel, Nowinski, Brent, Peddada, Shyamal, Knight, Rob
Publicado 2023

Normalization and microbial differential abundance strategies depend upon data characteristics

por Weiss, Sophie, Xu, Zhenjiang Zech, Peddada, Shyamal, Amir, Amnon, Bittinger, Kyle, Gonzalez, Antonio, Lozupone, Catherine, Zaneveld, Jesse R., Vázquez-Baeza, Yoshiki, Birmingham, Amanda, Hyde, Embriette R., Knight, Rob
Publicado 2017

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

por Weingarden, Alexa, González, Antonio, Vázquez-Baeza, Yoshiki, Weiss, Sophie, Humphry, Gregory, Berg-Lyons, Donna, Knights, Dan, Unno, Tatsuya, Bobr, Aleh, Kang, Johnthomas, Khoruts, Alexander, Knight, Rob, Sadowsky, Michael J
Publicado 2015

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

por Martino, Cameron, Shenhav, Liat, Marotz, Clarisse, Armstrong, George, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Morton, James T., Jiang, Lingjing, Dominguez-Bello, Maria Gloria, Swafford, Austin D., Halperin, Eran, Knight, Rob
Publicado 2020

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

por Martino, Cameron, McDonald, Daniel, Cantrell, Kalen, Dilmore, Amanda Hazel, Vázquez-Baeza, Yoshiki, Shenhav, Liat, Shaffer, Justin P., Rahman, Gibraan, Armstrong, George, Allaband, Celeste, Song, Se Jin, Knight, Rob
Publicado 2022

Temporal variability is a personalized feature of the human microbiome

por Flores, Gilberto E, Caporaso, J Gregory, Henley, Jessica B, Rideout, Jai Ram, Domogala, Daniel, Chase, John, Leff, Jonathan W, Vázquez-Baeza, Yoshiki, Gonzalez, Antonio, Knight, Rob, Dunn, Robert R, Fierer, Noah
Publicado 2014

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiom...

por Huang, Shi, Jiang, Shuaiming, Huo, Dongxue, Allaband, Celeste, Estaki, Mehrbod, Cantu, Victor, Belda-Ferre, Pedro, Vázquez-Baeza, Yoshiki, Zhu, Qiyun, Ma, Chenchen, Li, Congfa, Zarrinpar, Amir, Liu, Yang-Yu, Knight, Rob, Zhang, Jiachao
Publicado 2021

Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

por Zhu, Qiyun, Hou, Qiangchuan, Huang, Shi, Ou, Qianying, Huo, Dongxue, Vázquez-Baeza, Yoshiki, Cen, Chaoping, Cantu, Victor, Estaki, Mehrbod, Chang, Haibo, Belda-Ferre, Pedro, Kim, Ho-Cheol, Chen, Kaining, Knight, Rob, Zhang, Jiachao
Publicado 2021

Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

por Zhu, Qiyun, Hou, Qiangchuan, Huang, Shi, Ou, Qianying, Huo, Dongxue, Vázquez-Baeza, Yoshiki, Cen, Chaoping, Cantu, Victor, Estaki, Mehrbod, Chang, Haibo, Belda-Ferre, Pedro, Kim, Ho-Cheol, Chen, Kaining, Knight, Rob, Zhang, Jiachao
Publicado 2022

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

por Estaki, Mehrbod, Jiang, Lingjing, Bokulich, Nicholas A., McDonald, Daniel, González, Antonio, Kosciolek, Tomasz, Martino, Cameron, Zhu, Qiyun, Birmingham, Amanda, Vázquez‐Baeza, Yoshiki, Dillon, Matthew R., Bolyen, Evan, Caporaso, J. Gregory, Knight, Rob
Publicado 2020

Balance Trees Reveal Microbial Niche Differentiation

por Morton, James T., Sanders, Jon, Quinn, Robert A., McDonald, Daniel, Gonzalez, Antonio, Vázquez-Baeza, Yoshiki, Navas-Molina, Jose A., Song, Se Jin, Metcalf, Jessica L., Hyde, Embriette R., Lladser, Manuel, Dorrestein, Pieter C., Knight, Rob
Publicado 2017