phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data von McMurdie, Paul J, Holmes, Susan

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Waste not, want not: why rarefying microbiome data is inadmissible von McMurdie, Paul J, Holmes, Susan

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Exact sequence variants should replace operational taxonomic units in marker-gene data analysis von Callahan, Benjamin J, McMurdie, Paul J, Holmes, Susan P

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DADA2: High-resolution sample inference from Illumina amplicon data von Callahan, Benjamin J, McMurdie, Paul J, Rosen, Michael J, Han, Andrew W, Johnson, Amy Jo A, Holmes, Susan P

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Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking von McMurdie, Paul J, Holmes, Susan

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Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; peer review: 3 approved] von Callahan, Ben J, Sankaran, Kris, Fukuyama, Julia A, McMurdie, Paul J, Holmes, Susan P

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Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease von Stoeva, Magdalena K., Garcia-So, Jeewon, Justice, Nicholas, Myers, Julia, Tyagi, Surabhi, Nemchek, Madeleine, McMurdie, Paul J., Kolterman, Orville, Eid, John

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Temporal and spatial variation of the human microbiota during pregnancy von 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.

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Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer von Shah, Manasi S, DeSantis, Todd Z, Weinmaier, Thomas, McMurdie, Paul J, Cope, Julia L, Altrichter, Adam, Yamal, Jose-Miguel, Hollister, Emily B

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Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides von 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

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Normalization of Microbiome Profiling Data von McMurdie, Paul J.

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Increased circulating butyrate and ursodeoxycholate during probiotic intervention in humans with type 2 diabetes von McMurdie, Paul J, Stoeva, Magdalena K, Justice, Nicholas, Nemchek, Madeleine, Sieber, Christian M K, Tyagi, Surabhi, Gines, Jessica, Skennerton, Connor T, Souza, Michael, Kolterman, Orville, Eid, John

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Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides von McMurdie, Paul J, Hug, Laura A, Edwards, Elizabeth A, Holmes, Susan, Spormann, Alfred M

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Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation von Perraudeau, Fanny, McMurdie, Paul, Bullard, James, Cheng, Andrew, Cutcliffe, Colleen, Deo, Achal, Eid, John, Gines, Jessica, Iyer, Mohan, Justice, Nicholas, Loo, Wesley T, Nemchek, Madeleine, Schicklberger, Marcus, Souza, Michael, Stoneburner, Brendon, Tyagi, Surabhi, Kolterman, Orville

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Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column von BEHRENS, Sebastian, AZIZIAN, Mohammad F, MCMURDIE, Paul J, SABALOWSKY, Andrew, DOLAN, Mark E, SEMPRINI, Lew, SPORMANN, Alfred M

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

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Advancing Our Understanding of the Human Microbiome Using QIIME von 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

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Mo1807 Common Pharmaceuticals Shift in Gut Microbiome Composition von Iwai, Shoko, Han, Andrew, Kuczynski, Justin, McMurdie, Paul J, Steger, Rachel, DiStefano, Peter S, Mahmood, Nadir, DeSantis, Todd Z, Dabbagh, Karim

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Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species von McMurdie, Paul J, Behrens, Sebastian F, Holmes, Susan, Spormann, Alfred M

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Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; peer review: 3 approved] von Callahan, Ben J, Sankaran, Kris, Fukuyama, Julia A, McMurdie, Paul J, Holmes, Susan P

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