| phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data PJ McMurdie, S Holmes PloS one 8 (4), e61217, 2013 | 3042 | 2013 |
| DADA2: High-resolution sample inference from Illumina amplicon data. BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJA Johnson, ... Nature Methods, 2016 | 1547 | 2016 |
| Waste not, want not: why rarefying microbiome data is inadmissible PJ McMurdie, S Holmes PLoS computational biology 10 (4), e1003531, 2014 | 1065 | 2014 |
| Temporal and spatial variation of the human microbiota during pregnancy DB DiGiulio, BJ Callahan, PJ McMurdie, EK Costello, DJ Lyell, ... Proceedings of the National Academy of Sciences 112 (35), 11060-11065, 2015 | 383 | 2015 |
| Exact sequence variants should replace operational taxonomic units in marker-gene data analysis BJ Callahan, PJ McMurdie, SP Holmes The ISME journal 11 (12), 2639, 2017 | 375 | 2017 |
| Advancing our understanding of the human microbiome using QIIME JA Navas-Molina, JM Peralta-Sánchez, A González, PJ McMurdie, ... Methods in enzymology 531, 371-444, 2013 | 339 | 2013 |
| Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides PJ McMurdie, SF Behrens, JA Müller, J Göke, KM Ritalahti, R Wagner, ... PLoS Genetics 5 (11), e1000714, 2009 | 158 | 2009 |
| Bioconductor workflow for microbiome data analysis: from raw reads to community analyses BJ Callahan, K Sankaran, JA Fukuyama, PJ McMurdie, SP Holmes F1000Research 5, 2016 | 133 | 2016 |
| Monitoring abundance and expression of “Dehalococcoides” species chloroethene-reductive dehalogenases in a tetrachloroethene-dechlorinating flow column S Behrens, MF Azizian, PJ McMurdie, A Sabalowsky, ME Dolan, ... Appl. Environ. Microbiol. 74 (18), 5695-5703, 2008 | 123 | 2008 |
| Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data PJ McMURDIE, S Holmes Biocomputing 2012, 235-246, 2012 | 86 | 2012 |
| Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking PJ McMurdie, S Holmes Bioinformatics 31 (2), 282-283, 2014 | 55 | 2014 |
| Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides PJ McMurdie, LA Hug, EA Edwards, S Holmes, AM Spormann BMC genomics 12 (1), 287, 2011 | 54 | 2011 |
| Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay LC Burow, D Woebken, BM Bebout, PJ McMurdie, SW Singer, ... The ISME journal 6 (4), 863, 2012 | 47 | 2012 |
| Holmes PJ McMurdie S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics …, 2013 | 45 | 2013 |
| Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer MS Shah, TZ DeSantis, T Weinmaier, PJ McMurdie, JL Cope, A Altrichter, ... Gut 67 (5), 882-891, 2018 | 41 | 2018 |
| Comparisons of distance methods for combining covariates and abundances in microbiome studies J Fukuyama, PJ McMurdie, L Dethlefsen, DA Relman, S Holmes Biocomputing 2012, 213-224, 2012 | 36 | 2012 |
| Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species PJ McMurdie, SF Behrens, S Holmes, AM Spormann Appl. Environ. Microbiol. 73 (8), 2744-2747, 2007 | 34 | 2007 |
| DADA2: High resolution sample inference from amplicon data BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJ Johnson, SP Holmes bioRxiv, 024034, 2015 | 13 | 2015 |
| Microwave transmission line dielectric probe to detect biomolecular surface interactions Q Chen, J McMurdie, D Roitman, A Knoesen The 26th Annual International Conference of the IEEE Engineering in Medicine …, 2004 | 7 | 2004 |
| Preliminary study on different nutrient pools supplies for the phytoplankton growth in the Jiaozhou Bay in China in the fall of 2004 D Wang, J Sun, S Song, Q Luan, J McMurdie ACTA OCEANOLOGICA SINICA-ENGLISH EDITION- 26 (3), 110, 2007 | 1 | 2007 |
Susan P HolmesProfessor of Statistics, Stanford UniversityVerified email at stat.stanford.edu
