Paper · 23630581

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

McMurdie PJ and 1 other. PLoS One, 2013. Cited by 13,865 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. Papers, record 23630581. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/23630581

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.; PubMed
Journal: PLoS One; PubMed
Year: 2013; PubMed
Publication types: Journal Article, Research Support, N.I.H., Extramural; PubMed
PubMed: https://pubmed.ncbi.nlm.nih.gov/23630581/; PubMed
DOI: https://doi.org/10.1371/journal.pone.0061217; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC3632530/; PubMed
The journal: https://conductscience.org/library/journal-index/101285081; PubMed
Citations, by iCite: 13,865; iCite
Relative citation ratio, by iCite: 550; iCite
Revised in PubMed: 2024-09-24; PubMed

Authors2

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

Order	Author	Forename	Kind	ORCID iD
1	McMurdie PJ	Paul J
2	Holmes S	Susan

Source PubMed

Topics8

NLM's MeSH indexing of the paper, its major topics first.

MeSH term	Major
Metagenome	Major topic
Software	Major topic
Data Interpretation, Statistical
Humans
Multivariate Analysis
Phylogeny
Principal Component Analysis
Sequence Analysis, DNA

Source PubMed

Grants2

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes it	Agency	Country	NIH project	Stated by
R01 GM086884	NIGMS NIH HHS	United States	R01GM086884	PubMed and NIH
R01GM086884	NIGMS NIH HHS	United States	R01GM086884	PubMed and NIH

Source NIH RePORTER

Trials5

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

Trial	Title	The trial lists it as	Source
NCT04733456	Brain Activity and Oxygenation Inflammatory Bowel Disease (IBD) Patients	Background	ClinicalTrials.gov
NCT04765033	Trial on The Efficacy of Hypertonic Saline on Non-CF CSLD.	Results	ClinicalTrials.gov
NCT06069310	Mepolizumab Effectiveness in Patients With Chronic Rhinosinusitis, Nasal Polyps and Comorbid Severe Eosinophilic Asthma	Background	ClinicalTrials.gov
NCT06513026	Milk for Diabetes Prevention	Background	ClinicalTrials.gov
NCT07169123	Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD	Background	ClinicalTrials.gov

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References48

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

Order	PMID	Title	Journal	Year	In Papers	Source
1	16,731,699	Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.	Bioinformatics	2006	https://conductscience.org/library/papers/16731699	PubMed
2	15,001,713	Environmental genome shotgun sequencing of the Sargasso Sea.	Science	2004	https://conductscience.org/library/papers/15001713	PubMed
3	22,692,220	mcaGUI: microbial community analysis R-Graphical User Interface (GUI).	Bioinformatics	2012	https://conductscience.org/library/papers/22692220	PubMed
4	16,820,507	Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.	Appl Environ Microbiol	2006	https://conductscience.org/library/papers/16820507	PubMed
5	19,710,709	Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.	ISME J	2010	https://conductscience.org/library/papers/19710709	PubMed
6	17,947,321	SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.	Nucleic Acids Res	2007	https://conductscience.org/library/papers/17947321	PubMed
7	9,115,194	A molecular view of microbial diversity and the biosphere.	Science	1997	https://conductscience.org/library/papers/9115194	PubMed
8	20,944,712	Computational science: ...Error.	Nature	2010	https://conductscience.org/library/papers/20944712	PubMed
9	20,944,687	Publish your computer code: it is good enough.	Nature	2010	https://conductscience.org/library/papers/20944687	PubMed
10	22,699,609	Structure, function and diversity of the healthy human microbiome.	Nature	2012	https://conductscience.org/library/papers/22699609	PubMed

1 to 10 of 48

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Cited by10,656

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 13,865 citations.

PMID	Title	Journal	Year	In Papers	Source
42,989,121	Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss).	BMC Microbiol	2026	https://conductscience.org/library/papers/42989121	PubMed
42,984,320	Biogeographic Barriers and Gut Microbiome Turnover Across the Peromyscus maniculatus Species Complex.	Mol Ecol	2026	https://conductscience.org/library/papers/42984320	PubMed
42,983,601	Host phenology drives directional assembly of the fruit endophytic mycobiome and precedes disease-associated community dominance in cranberry.	Environ Microbiome	2026	https://conductscience.org/library/papers/42983601	PubMed
42,983,092	Synergy in viral-bacterial co-infection expedites algal bloom demise.	Nature	2026	https://conductscience.org/library/papers/42983092	PubMed
42,982,861	FMT combined with atezolizumab-bevacizumab in hepatocellular carcinoma refractory to immunotherapy: an open label, single-arm, phase II pilot study.	Nat Commun	2026	https://conductscience.org/library/papers/42982861	PubMed
42,982,796	Gut and oral microbiota composition is associated with psychopathic personality: a cross-sectional study.	Transl Psychiatry	2026	https://conductscience.org/library/papers/42982796	PubMed
42,980,823	Flood-Driven Salinity Shifts Restructure Estuarine Pico-Sized Chlorophyte Assemblages at a Subtropical River-Sea Interface.	Microb Ecol	2026	https://conductscience.org/library/papers/42980823	PubMed
42,980,664	Fusarium Community Composition and Co-Occurrence with Other Fungi and Bacteria in Finnish Oat Crop.	Microb Ecol	2026	https://conductscience.org/library/papers/42980664	PubMed
42,979,488	Fungal response to drought in the maize rhizosphere after reusing cover crop root channels.	ISME Commun	2026	https://conductscience.org/library/papers/42979488	PubMed
42,979,227	Genome-resolved metagenomics reveals nonmethanogenic soil lineages in an Andean páramo wetland.	ISME Commun	2026	https://conductscience.org/library/papers/42979227	PubMed

1 to 10 of 10,656

See all 10,656 cited by

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed: 2026-11-06; PubMed
iCite: 2026-11-05; iCite
PMC's ID file: 2026-11-05; PMC's ID file
NIH RePORTER's grant and paper links: 2026-11-01; NIH RePORTER's grant and paper links
Trials: 2026-11-12
Gene search: 2026-11-11
Pipelines: 2026-09-18

Sources 11

ChEMBL, through Open TargetsCC BY-SA 3.0
ClinicalTrials.govNo license stated
HGNCCC0
iCiteCC BY 4.0
NCBI GenePublic domain (US government)
NIH RePORTER's grant and paper linksPublic domain
Open TargetsCC0 1.0
PMC's ID filePublic domain (US government)
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0

Each source's terms

ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
ClinicalTrials.govnone stated
HGNCCC0: https://www.genenames.org/about/license/
iCiteCC BY 4.0
NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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