| DADA2: High-resolution sample inference from Illumina amplicon data. BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJA Johnson, ... Nature Methods, 2016 | 25207 | 2016 |
| phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data PJ McMurdie, S Holmes PloS one 8 (4), e61217, 2013 | 17144 | 2013 |
| Exact sequence variants should replace operational taxonomic units in marker-gene data analysis BJ Callahan, PJ McMurdie, SP Holmes The ISME journal 11 (12), 2639-2643, 2017 | 3106 | 2017 |
| Waste not, want not: why rarefying microbiome data is inadmissible PJ McMurdie, S Holmes PLoS computational biology 10 (4), e1003531, 2014 | 2939 | 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 | 1217 | 2015 |
| 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 | 1020 | 2016 |
| 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 | 658 | 2013 |
| Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data PJ McMURDIE, S Holmes Biocomputing 2012, 235-246, 2012 | 306 | 2012 |
| Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease MK Stoeva, J Garcia-So, N Justice, J Myers, S Tyagi, M Nemchek, ... Gut microbes 13 (1), 1907272, 2021 | 251 | 2021 |
| Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease FJ Ryan, AM Ahern, RS Fitzgerald, EJ Laserna-Mendieta, EM Power, ... Nature communications 11 (1), 1512, 2020 | 246 | 2020 |
| 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 | 193 | 2009 |
| 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 | 177 | 2018 |
| 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, ... Applied and Environmental Microbiology 74 (18), 5695-5703, 2008 | 166 | 2008 |
| Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking PJ McMurdie, S Holmes Bioinformatics 31 (2), 282-283, 2015 | 163 | 2015 |
| Holmes PJ McMurdie | 153 | 2013 |
| High-resolution sample inference from Illumina amplicon data., 2016, 13 BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJA Johnson, SPH Dada DOI: https://doi. org/10.1038/nmeth 3869, 581-583, 0 | 152 | |
| Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation F Perraudeau, P McMurdie, J Bullard, A Cheng, C Cutcliffe, A Deo, J Eid, ... BMJ Open Diabetes Research and Care 8 (1), e001319, 2020 | 119 | 2020 |
| DADA2: High resolution sample inference from amplicon data BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJ Johnson, SP Holmes BioRxiv, 024034, 2015 | 78 | 2015 |
| 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, 1-15, 2011 | 74 | 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), 863-874, 2012 | 70 | 2012 |
Susan P HolmesProfessor of Statistics, Stanford UniversityVerified email at stat.stanford.edu
