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1,427 results
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phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
McMurdie PJ, Holmes S. McMurdie PJ, et al. Among authors: holmes s. PLoS One. 2013 Apr 22;8(4):e61217. doi: 10.1371/journal.pone.0061217. Print 2013. PLoS One. 2013. PMID: 23630581 Free PMC article.
Gene expression network analysis and applications to immunology.
Nacu S, Critchley-Thorne R, Lee P, Holmes S. Nacu S, et al. Among authors: holmes s. Bioinformatics. 2007 Apr 1;23(7):850-8. doi: 10.1093/bioinformatics/btm019. Epub 2007 Jan 31. Bioinformatics. 2007. PMID: 17267429
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. McMurdie PJ, et al. Among authors: holmes s. PLoS Genet. 2009 Nov;5(11):e1000714. doi: 10.1371/journal.pgen.1000714. Epub 2009 Nov 6. PLoS Genet. 2009. PMID: 19893622 Free PMC article.
Quantitative, architectural analysis of immune cell subsets in tumor-draining lymph nodes from breast cancer patients and healthy lymph nodes.
Setiadi AF, Ray NC, Kohrt HE, Kapelner A, Carcamo-Cavazos V, Levic EB, Yadegarynia S, van der Loos CM, Schwartz EJ, Holmes S, Lee PP. Setiadi AF, et al. Among authors: holmes s. PLoS One. 2010 Aug 25;5(8):e12420. doi: 10.1371/journal.pone.0012420. PLoS One. 2010. PMID: 20811638 Free PMC article.
Visualization and statistical comparisons of microbial communities using R packages on Phylochip data.
Holmes S, Alekseyenko A, Timme A, Nelson T, Pasricha PJ, Spormann A. Holmes S, et al. Pac Symp Biocomput. 2011:142-53. doi: 10.1142/9789814335058_0016. Pac Symp Biocomput. 2011. PMID: 21121042 Free PMC article.
An Interactive Java Statistical Image Segmentation System: GemIdent.
Holmes S, Kapelner A, Lee PP. Holmes S, et al. J Stat Softw. 2009 Jun 1;30(10):i10. J Stat Softw. 2009. PMID: 21614138 Free PMC article.
Comparisons of distance methods for combining covariates and abundances in microbiome studies.
Fukuyama J, McMurdie PJ, Dethlefsen L, Relman DA, Holmes S. Fukuyama J, et al. Among authors: holmes s. Pac Symp Biocomput. 2012:213-24. Pac Symp Biocomput. 2012. PMID: 22174277 Free PMC article.
Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.
McMurdie PJ, Holmes S. McMurdie PJ, et al. Among authors: holmes s. Pac Symp Biocomput. 2012:235-46. Pac Symp Biocomput. 2012. PMID: 22174279 Free PMC article.
De la Cruz O, Holmes S. De la Cruz O, et al. Among authors: holmes s. Ann Appl Stat. 2011 Dec;5(4):2266-2277. doi: 10.1214/10-aoas408. Ann Appl Stat. 2011. PMID: 22282721 Free PMC article.
Denoising PCR-amplified metagenome data.
Rosen MJ, Callahan BJ, Fisher DS, Holmes SP. Rosen MJ, et al. Among authors: holmes sp. BMC Bioinformatics. 2012 Oct 31;13:283. doi: 10.1186/1471-2105-13-283. BMC Bioinformatics. 2012. PMID: 23113967 Free PMC article.
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