PHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATA

Por McMURDIE, PAUL J., HOLMES, SUSAN
Publicado em 2012

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Por McMurdie, Paul J., Holmes, Susan
Publicado em 2013

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Por McMurdie, Paul J., Holmes, Susan
Publicado em 2014

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

Por McMurdie, Paul J., Holmes, Susan
Publicado no Bioinformatics (2015)

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

Por Callahan, Benjamin J, McMurdie, Paul J, Holmes, Susan P
Publicado no ISME J (2017)

Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species

Por McMurdie, Paul J., Behrens, Sebastian F., Holmes, Susan, Spormann, Alfred M.
Publicado em 2007

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

Por McMurdie, Paul J, Hug, Laura A, Edwards, Elizabeth A, Holmes, Susan, Spormann, Alfred M
Publicado em 2011

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

Por Callahan, Ben J., Sankaran, Kris, Fukuyama, Julia A., McMurdie, Paul J., Holmes, Susan P.
Publicado no F1000Res (2016)

Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column

Por Behrens, Sebastian, Azizian, Mohammad F., McMurdie, Paul J., Sabalowsky, Andrew, Dolan, Mark E., Semprini, Lew, Spormann, Alfred M.
Publicado em 2008

DADA2: High resolution sample inference from Illumina amplicon data

Por Callahan, Benjamin J, McMurdie, Paul J, Rosen, Michael J, Han, Andrew W, Johnson, Amy Jo A, Holmes, Susan P
Publicado no Nat Methods (2016)

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Por McMurdie, Paul J., Behrens, Sebastian F., Müller, Jochen A., Göke, Jonathan, Ritalahti, Kirsti M., Wagner, Ryan, Goltsman, Eugene, Lapidus, Alla, Holmes, Susan, Löffler, Frank E., Spormann, Alfred M.
Publicado em 2009

Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay

Por Burow, Luke C, Woebken, Dagmar, Bebout, Brad M, McMurdie, Paul J, Singer, Steven W, Pett-Ridge, Jennifer, Prufert-Bebout, Leslie, Spormann, Alfred M, Weber, Peter K, Hoehler, Tori M
Publicado em 2012

Temporal and spatial variation of the human microbiota during pregnancy

Por DiGiulio, Daniel B., Callahan, Benjamin J., McMurdie, Paul J., Costello, Elizabeth K., Lyell, Deirdre J., Robaczewska, Anna, Sun, Christine L., Goltsman, Daniela S. A., Wong, Ronald J., Shaw, Gary, Stevenson, David K., Holmes, Susan P., Relman, David A.
Publicado no Proc Natl Acad Sci U S A (2015)

Advancing our understanding of the human microbiome using QIIME

Por Navas-Molina, José A., Peralta-Sánchez, Juan M., González, Antonio, McMurdie, Paul J., Vázquez-Baeza, Yoshiki, Xu, Zhenjiang, Ursell, Luke K., Lauber, Christian, Zhou, Hongwei, Song, Se Jin, Huntley, James, Ackermann, Gail L., Berg-Lyons, Donna, Holmes, Susan, Caporaso, J. Gregory, Knight, Rob
Publicado no Methods Enzymol (2013)