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Year Number of Results
2010 3
2011 4
2012 5
2013 2
2020 0
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14 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. PLoS One. 2013 Apr 22;8(4):e61217. doi: 10.1371/journal.pone.0061217. Print 2013. PLoS One. 2013. PMID: 23630581 Free PMC article.
Denoising PCR-amplified metagenome data.
Rosen MJ, Callahan BJ, Fisher DS, Holmes SP. Rosen MJ, et al. BMC Bioinformatics. 2012 Oct 31;13:283. doi: 10.1186/1471-2105-13-283. BMC Bioinformatics. 2012. PMID: 23113967 Free PMC article.
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. Navas-Molina JA, et al. Methods Enzymol. 2013;531:371-444. doi: 10.1016/B978-0-12-407863-5.00019-8. Methods Enzymol. 2013. PMID: 24060131 Free PMC article.
The molecular architecture of the eukaryotic chaperonin TRiC/CCT.
Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. Leitner A, et al. Structure. 2012 May 9;20(5):814-25. doi: 10.1016/j.str.2012.03.007. Epub 2012 Apr 12. Structure. 2012. PMID: 22503819 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. Pac Symp Biocomput. 2012:213-24. Pac Symp Biocomput. 2012. PMID: 22174277 Free PMC article.
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.
Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML. Doherty KM, et al. BMC Bioinformatics. 2011 Dec 15;12:477. doi: 10.1186/1471-2105-12-477. BMC Bioinformatics. 2011. PMID: 22172090 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. Pac Symp Biocomput. 2012:235-46. Pac Symp Biocomput. 2012. PMID: 22174279 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.
Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.
McMurdie PJ, Hug LA, Edwards EA, Holmes S, Spormann AM. McMurdie PJ, et al. BMC Genomics. 2011 Jun 2;12:287. doi: 10.1186/1471-2164-12-287. BMC Genomics. 2011. PMID: 21635780 Free PMC article.
Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations.
Reuman EC, Rhee SY, Holmes SP, Shafer RW. Reuman EC, et al. J Antimicrob Chemother. 2010 Jul;65(7):1477-85. doi: 10.1093/jac/dkq140. Epub 2010 May 12. J Antimicrob Chemother. 2010. PMID: 20462946 Free PMC article.
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