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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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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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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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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Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease von Ryan, F. J., Ahern, A. M., Fitzgerald, R. S., Laserna-Mendieta, E. J., Power, E. M., Clooney, A. G., O’Donoghue, K. W., McMurdie, P. J., Iwai, S., Crits-Christoph, A., Sheehan, D., Moran, C., Flemer, B., Zomer, A. L., Fanning, A., O’Callaghan, J., Walton, J., Temko, A., Stack, W., Jackson, L., Joyce, S. A., Melgar, S., DeSantis, T. Z., Bell, J. T., Shanahan, F., Claesson, M. J.

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Stratiform Precipitation Processes in Cyclones Passing over a Coastal Mountain Range von Zagrodnik, Joseph P., McMurdie, Lynn A., Houze, Robert A.

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Simulated particle evolution within a winter storm: contributions of riming to radar moments and precipitation fallout von DeLaFrance, Andrew, McMurdie, Lynn A, Rowe, Angela K, Heymsfield, Andrew J

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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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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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THE OLYMPIC MOUNTAINS EXPERIMENT (OLYMPEX) von Houze, Robert A., McMurdie, Lynn A., Petersen, Walter A., Schwaller, Mathew R., Baccus, William, Lundquist, Jessica D., Mass, Clifford F., Nijssen, Bart, Rutledge, Steven A., Hudak, David R., Tanelli, Simone, Mace, Gerald G., Poellot, Michael R., Lettenmaier, Dennis P., Zagrodnik, Joseph P., Rowe, Angela K., DeHart, Jennifer C., Madaus, Luke E., Barnes, Hannah C.

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Improving Simulations of Warm Rain in a Bulk Microphysics Scheme von Conrick, Robert, Mass, Clifford F., McMurdie, Lynn

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Investigation of Microphysical Properties within Regions of Enhanced Dual-Frequency Ratio during the IMPACTS Field Campaign von Finlon, Joseph A., McMurdie, Lynn A., Chase, Randy J.

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Vertical Structure and Microphysical Characteristics of Frontal Systems Passing over a Three-Dimensional Coastal Mountain Range von Zagrodnik, Joseph P., McMurdie, Lynn A., Houze, Robert A., Tanelli, Simone

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On frame synchronization in aeronautical telemetry von Rice, Michael, Mcmurdie, Andrew

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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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Normalization of Microbiome Profiling Data von McMurdie, Paul J.

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