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Items: 17

1.

Normalization of Microbiome Profiling Data.

McMurdie PJ.

Methods Mol Biol. 2018;1849:143-168. doi: 10.1007/978-1-4939-8728-3_10.

PMID:
30298253
2.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.

Callahan BJ, McMurdie PJ, Holmes SP.

ISME J. 2017 Dec;11(12):2639-2643. doi: 10.1038/ismej.2017.119. Epub 2017 Jul 21.

3.

Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer.

Shah MS, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal JM, Hollister EB.

Gut. 2018 May;67(5):882-891. doi: 10.1136/gutjnl-2016-313189. Epub 2017 Mar 24.

PMID:
28341746
4.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP.

Version 2. F1000Res. 2016 Jun 24 [revised 2016 Jan 1];5:1492. eCollection 2016.

5.

DADA2: High-resolution sample inference from Illumina amplicon data.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP.

Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23.

6.

Temporal and spatial variation of the human microbiota during pregnancy.

DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A, Sun CL, Goltsman DS, Wong RJ, Shaw G, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11060-5. doi: 10.1073/pnas.1502875112. Epub 2015 Aug 17.

7.

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

McMurdie PJ, Holmes S.

Bioinformatics. 2015 Jan 15;31(2):282-3. doi: 10.1093/bioinformatics/btu616. Epub 2014 Sep 26.

8.

Waste not, want not: why rarefying microbiome data is inadmissible.

McMurdie PJ, Holmes S.

PLoS Comput Biol. 2014 Apr 3;10(4):e1003531. doi: 10.1371/journal.pcbi.1003531. eCollection 2014 Apr.

9.

Advancing our understanding of the human microbiome using QIIME.

Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R.

Methods Enzymol. 2013;531:371-444. doi: 10.1016/B978-0-12-407863-5.00019-8.

10.

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

McMurdie PJ, Holmes S.

PLoS One. 2013 Apr 22;8(4):e61217. doi: 10.1371/journal.pone.0061217. Print 2013.

11.
12.

Comparisons of distance methods for combining covariates and abundances in microbiome studies.

Fukuyama J, McMurdie PJ, Dethlefsen L, Relman DA, Holmes S.

Pac Symp Biocomput. 2012:213-24.

13.

Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay.

Burow LC, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM.

ISME J. 2012 Apr;6(4):863-74. doi: 10.1038/ismej.2011.142. Epub 2011 Oct 20.

14.

Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.

McMurdie PJ, Hug LA, Edwards EA, Holmes S, Spormann AM.

BMC Genomics. 2011 Jun 2;12:287. doi: 10.1186/1471-2164-12-287.

15.

Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.

McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM.

PLoS Genet. 2009 Nov;5(11):e1000714. doi: 10.1371/journal.pgen.1000714. Epub 2009 Nov 6.

16.

Monitoring abundance and expression of "Dehalococcoides" species chloroethene-reductive dehalogenases in a tetrachloroethene-dechlorinating flow column.

Behrens S, Azizian MF, McMurdie PJ, Sabalowsky A, Dolan ME, Semprini L, Spormann AM.

Appl Environ Microbiol. 2008 Sep;74(18):5695-703. doi: 10.1128/AEM.00926-08. Epub 2008 Aug 1.

17.

Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species.

McMurdie PJ, Behrens SF, Holmes S, Spormann AM.

Appl Environ Microbiol. 2007 Apr;73(8):2744-7. Epub 2007 Feb 16.

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