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Paul J McMurdie
Paul J McMurdie
Principal Bioinformatics Scientist at D2G Oncology
Verified email at d2g-oncology.com - Homepage
Title
Cited by
Cited by
Year
DADA2: High-resolution sample inference from Illumina amplicon data.
BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJA Johnson, ...
Nature Methods, 2016
198162016
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
PJ McMurdie, S Holmes
PloS one 8 (4), e61217, 2013
143712013
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
27332017
Waste not, want not: why rarefying microbiome data is inadmissible
PJ McMurdie, S Holmes
PLoS computational biology 10 (4), e1003531, 2014
27062014
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
11062015
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
8852016
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
6282013
Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data
PJ McMURDIE, S Holmes
Biocomputing 2012, 235-246, 2012
2802012
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
1972020
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
1912009
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
1742021
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
1592008
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
1582018
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
PJ McMurdie, S Holmes
Bioinformatics 31 (2), 282-283, 2015
1422015
Holmes
PJ McMurdie
1362013
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
872020
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
702011
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
69
DADA2: High resolution sample inference from amplicon data
BJ Callahan, PJ McMurdie, MJ Rosen, AW Han, AJ Johnson, SP Holmes
BioRxiv, 024034, 2015
662015
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
652012
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