Ten quick tips for effective dimensionality reduction von Nguyen, Lan Huong, 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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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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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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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data von Davis, Nicole M, Proctor, Diana M, Holmes, Susan P, Relman, David A, Callahan, Benjamin J

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Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle von Gorvitovskaia, Anastassia, Holmes, Susan P, Huse, Susan M

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Latent variable modeling for the microbiome von Sankaran, Kris, Holmes, Susan P

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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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Multitable Methods for Microbiome Data Integration von Sankaran, Kris, Holmes, Susan P.

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Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women von Callahan, Benjamin J., DiGiulio, Daniel B., Goltsman, Daniela S. Aliaga, Sun, Christine L., Costello, Elizabeth K., Jeganathan, Pratheepa, Biggio, Joseph R., Wong, Ronald J., Druzin, Maurice L., Shaw, Gary M., Stevenson, David K., Holmes, Susan P., Relman, David A.

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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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Frontal fibrosing alopecia: A review of 60 cases von MacDonald, Alison, MRCP, Clark, Colin, FRCP, Holmes, Susan, FRCP, MD

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Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences von Tzou, Philip L., Pond, Sergei L. Kosakovsky, Avila-Rios, Santiago, Holmes, Susan P., Kantor, Rami, Shafer, Robert W.

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Profiling the human intestinal environment under physiological conditions von Shalon, Dari, Culver, Rebecca Neal, Grembi, Jessica A., Folz, Jacob, Treit, Peter V., Shi, Handuo, Rosenberger, Florian A., Dethlefsen, Les, Meng, Xiandong, Yaffe, Eitan, Aranda-Díaz, Andrés, Geyer, Philipp E., Mueller-Reif, Johannes B., Spencer, Sean, Patterson, Andrew D., Triadafilopoulos, George, Holmes, Susan P., Mann, Matthias, Fiehn, Oliver, Relman, David A., Huang, Kerwyn Casey

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Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time von Hoy, Yana Emmy, Bik, Elisabeth M, Lawley, Trevor D, Holmes, Susan P, Monack, Denise M, Theriot, Julie A, Relman, David A

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Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment von Fukuyama, Julia, Rumker, Laurie, Sankaran, Kris, Jeganathan, Pratheepa, Dethlefsen, Les, Relman, David A, Holmes, Susan P

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A Statistical Perspective on the Challenges in Molecular Microbial Biology von Jeganathan, Pratheepa, Holmes, Susan P.

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Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth von Costello, Elizabeth K., DiGiulio, Daniel B., Robaczewska, Anna, Symul, Laura, Wong, Ronald J., Shaw, Gary M., Stevenson, David K., Holmes, Susan P., Kwon, Douglas S., Relman, David A.

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Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea von Bik, Elisabeth M., Costello, Elizabeth K., Switzer, Alexandra D., Callahan, Benjamin J., Holmes, Susan P., Wells, Randall S., Carlin, Kevin P., Jensen, Eric D., Venn-Watson, Stephanie, Relman, David A.

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