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Paul J. McMurdie
Researcher at Stanford University
Publications - 29
Citations - 33660
Paul J. McMurdie is an academic researcher from Stanford University. The author has contributed to research in topics: Dehalococcoides & Bioconductor. The author has an hindex of 20, co-authored 26 publications receiving 19880 citations.
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Journal ArticleDOI
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan,Paul J. McMurdie,Michael J. Rosen,Andrew W. Han,Amy Jo A. Johnson,Susan Holmes +5 more
TL;DR: The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants.
Journal ArticleDOI
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 more
TL;DR: The phyloseq project for R is a new open-source software package dedicated to the object-oriented representation and analysis of microbiome census data in R, which supports importing data from a variety of common formats, as well as many analysis techniques.
Journal ArticleDOI
Waste not, want not: why rarefying microbiome data is inadmissible.
Paul J. McMurdie,Susan Holmes +1 more
TL;DR: It is advocated that investigators avoid rarefying altogether and supported statistical theory is provided that simultaneously accounts for library size differences and biological variability using an appropriate mixture model.
Journal ArticleDOI
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.
TL;DR: It is argued that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
Journal ArticleDOI
Temporal and spatial variation of the human microbiota during pregnancy
Daniel B. DiGiulio,Benjamin J. Callahan,Paul J. McMurdie,Elizabeth K. Costello,Deirdre J. Lyell,Anna Robaczewska,Christine L. Sun,Daniela S. Aliaga Goltsman,Ronald J. Wong,Gary M. Shaw,David K. Stevenson,Susan Holmes,David A. Relman +12 more
TL;DR: It is suggested that pregnancy outcomes might be predicted by features of the microbiota early in gestation, as well as the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.