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Paul J. McMurdie · SciRah

Researcher profile · OpenAlex

Paul J. McMurdie

Stanford University
Departments of Civil and Environmental Engineering and of Chemical Engineering, Stanford University, Stanford, California, United States of America
US
Big Health Inc. (United States)
Departments of Civil and Environmental Engineering and of Chemical Engineering, Stanford University, Stanford, California, United States of America
US

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Paul J. McMurdie — researcher profile on SciRah

ORCID iD 0000-0001-8879-3954

Citations: 68.3K
h-index: 21
i10-index: 22
Works: 49

From OpenAlex.

Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

Most-cited papers

DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen, Andrew Han +2 more
2016Nature Methods35K citations Open access
OpenAlex
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Paul J. McMurdie, Susan Holmes
2013PLoS ONE21K citations Open access
OpenAlex
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Benjamin J. Callahan, Paul J. McMurdie, Susan Holmes
2017The ISME Journal3,311 citations Open access
OpenAlex
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Paul J. McMurdie, Susan Holmes
2014PLoS Computational Biology2,928 citations Open access
OpenAlex
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Benjamin J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie +1 more
2016F1000Research1,130 citations Open access
OpenAlex
Temporal and spatial variation of the human microbiota during pregnancy
Daniel B. DiGiulio, Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello +9 more
2015Proceedings of the National Academy of Sciences1,129 citations Open access
OpenAlex
Advancing Our Understanding of the Human Microbiome Using QIIME
Jose Antonio Navas-Molina, Juan Manuel Peralta‐Sánchez, Antonio González, Paul J. McMurdie +12 more
2013Methods in enzymology on CD-ROM/Methods in enzymology610 citations Open access
OpenAlex
Butyrate-producing human gut symbiont, Clostridium butyricum , and its role in health and disease
Magdalena K. Stoeva, Jeewon Garcia-So, Nicholas Justice, Julia N. Myers +5 more
2021Gut Microbes519 citations Open access
OpenAlex
Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease
Feargal J. Ryan, Anna M. Ahern, Rachel S. Fitzgerald, Emilio José Laserna Mendieta +22 more
2020Nature Communications286 citations Open access
OpenAlex
Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.
Paul J. McMurdie, Susan Holmes
2012PubMed244 citations Open access
OpenAlex
PHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATA
Paul J. McMurdie, Susan Holmes
2011Pacific Symposium on Biocomputing (PSB)196 citations
OpenAlex
Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation
Fanny Perraudeau, Paul J. McMurdie, James Bullard, Andrew Cheng +13 more
2020BMJ Open Diabetes Research & Care183 citations Open access
OpenAlex
Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer
Manasi S. Shah, Todd Z. DeSantis, Thomas Weinmaier, Paul J. McMurdie +4 more
2017Gut180 citations
OpenAlex
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Paul J. McMurdie, Susan Holmes
2014Bioinformatics164 citations Open access
OpenAlex
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
Paul J. McMurdie, Sebastian Behrens, Jochen A. Müller, Jonathan Göke +7 more
2016Figshare158 citations Open access
OpenAlex
Monitoring Abundance and Expression of “ Dehalococcoides ” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
Sebastian Behrens, Mohammad F. Azizian, Paul J. McMurdie, Andrew R. Sabalowsky +3 more
2008Applied and Environmental Microbiology136 citations Open access
OpenAlex
Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides
Paul J. McMurdie, Laura A. Hug, Elizabeth Anne Edwards, Susan Holmes +1 more
2011BMC Genomics60 citations Open access
OpenAlex
Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay
Luke C. Burow, Dagmar Woebken, Brad M. Bebout, Paul J. McMurdie +6 more
2011The ISME Journal57 citations Open access
OpenAlex
COMPARISONS OF DISTANCE METHODS FOR COMBINING COVARIATES AND ABUNDANCES IN MICROBIOME STUDIES
Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman +1 more
2011Pacific Symposium on Biocomputing (PSB)54 citations Open access
OpenAlex
Increased circulating butyrate and ursodeoxycholate during probiotic intervention in humans with type 2 diabetes
Paul J. McMurdie, Magdalena K. Stoeva, Nicholas Justice, Madeleine P. Nemchek +7 more
2022BMC Microbiology50 citations Open access
OpenAlex
Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species
Paul J. McMurdie, Sebastian Behrens, Susan Holmes, Alfred Michael Spormann
2007Applied and Environmental Microbiology27 citations Open access
OpenAlex
Normalization of Microbiome Profiling Data
Paul J. McMurdie
2018Methods in molecular biology11 citations
OpenAlex
41-LB: Changes in Circulating Metabolites, Including Butyrate, Points to Underlying Mechanism of a Probiotic Intervention That Improves Postprandial Hyperglycemia in Subjects with Type 2 Diabetes
Paul J. McMurdie, Magdalena K. Stoeva, Madeleine P. Nemchek, Surabhi Tyagi +3 more
2021Diabetes1 citations
OpenAlex
Evaluation of completeness of commonly used data elements for clinical trial eligibility criteria using a registry-enhanced data collection process: Results from patients with non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) at three community oncology practices.
Annette Campbell Fontaine, Barbara L. McAneny, Valerie Tucker, Michael Zach Koontz +7 more
2024JCO Oncology Practice0 citations
OpenAlex
Abstract 2789: Tumor suppressor genotype dramatically impacts lung cancer response to KRAS G12C inhibitors in vivo
Paul J. McMurdie, Ian P. Winters, Lily M. Blair, Lafia Sebastian +10 more
2023Cancer Research0 citations
OpenAlex
758-P: Medical Food (MF) with Butyrate Producing (BP)+Mucin Regulating (MR) Microbes Improves Glucose Control (GC) in T2D
Orville Kolterman, Fanny Perraudeau, Mohan Iyer, John S. Eid +9 more
2019Diabetes0 citations
OpenAlex
Peer Review Report For: Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; peer review: 3 approved]
Benjamin J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie +1 more
20160 citations Open access
OpenAlex
Peer Review Report For: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; peer review: 3 approved]
Benjamin J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie +1 more
20160 citations Open access
OpenAlex
Peer Review Report For: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; peer review: 3 approved]
Benjamin J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie +1 more
20160 citations Open access
OpenAlex
Mo1807 Common Pharmaceuticals Shift in Gut Microbiome Composition
Shoko Iwai, Andrew Han, Justin Kuczynski, Paul J. McMurdie +5 more
2015Gastroenterology0 citations Open access
OpenAlex
Version 1.8.2 Date 2014-05-23
Paul J. McMurdie, From Gregory Jordan, Scott Chamberlain, R Topics Documented
20140 citations
OpenAlex
Advancing Our Understanding of the Human Microbiome Using QIIME
Ibrahima DIALLO, Juan Manuel Peralta‐Sánchez, Antonio Gonzalez, Paul J. McMurdie +12 more
2013Zenodo (CERN European Organization for Nuclear Research)0 citations Open access
OpenAlex
Version 1.4.5 Date 2013-09-17
Paul J. McMurdie, From Gregory Jordan, Scott Chamberlain
20130 citations
OpenAlex
Version 1.5.17 Date 2013-05-22
Paul J. McMurdie, From Gregory Jordan, Scott Chamberlain
20130 citations
OpenAlex
Version 1.4.4 Date 2013-05-22
Paul J. McMurdie, From Gregory Jordan, Scott Chamberlain
20130 citations
OpenAlex
Spatial variation in microbial controls on soil organic matter turnover relative to preferential flow paths
Yoko Masue‐Slowey, K. Dhiman, Paul J. McMurdie, Scott E. Fendorf +1 more
2012AGU Fall Meeting Abstracts0 citations
OpenAlex
UniFrac and double principal coordinates analysis
Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman +1 more
2012F1000Research0 citations Open access
OpenAlex
NanoSIP: Developing Community Imaging for Phylogenetic and Functional Characterization Using Cyanobacterial Mats
S W Singer, Paul J. McMurdie, Peter M. Weber
2011OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)0 citations
OpenAlex
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
Paul J. McMurdie, Sebastian Behrens, Jochen A. Müller, Jonathan Göke +7 more
2009PLoS Genetics0 citations Open access
OpenAlex

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20122024

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Susan HolmesStanford University×20
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Susan Holmes — researcher profile on SciRah
Benjamin J. CallahanStanford University×7
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Benjamin J. Callahan — researcher profile on SciRah
Julia FukuyamaStanford University×6
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Julia Fukuyama — researcher profile on SciRah
Alfred Michael Spormann

Stanford University

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Surabhi TyagiPendulum Therapeutics, Inc×5

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Orville KoltermanPendulum Therapeutics, Inc×5

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John S. EidPendulum Therapeutics, Inc×5

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Kris SankaranStanford University×4

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Nicholas JusticePendulum Therapeutics, Inc×4

Madeleine P. NemchekPendulum Therapeutics, Inc×4

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Jessica GinesPendulum Therapeutics, Inc, San Francisco, California, USA×4

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Sebastian BehrensStanford University×4

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Affiliation history

March of Dimes2015
Second Genome (United States)2016–2020
Stanford Medicine2015
Big Health Inc. (United States)2016
Stanford University2008–2016