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Journal of Healthcare Engineering
Volume 2017, Article ID 5284145, 7 pages
https://doi.org/10.1155/2017/5284145
Research Article

2-Way k-Means as a Model for Microbiome Samples

1Department of Computer Science, Columbia University, New York, NY 10027, USA
2Department of Biological Sciences, Columbia University, New York, NY 10027, USA

Correspondence should be addressed to Weston J. Jackson; moc.liamg@noskcaj.j.notsew

Received 20 May 2017; Accepted 17 July 2017; Published 5 September 2017

Academic Editor: Ahmad P. Tafti

Copyright © 2017 Weston J. Jackson et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Human Microbiome Project Consortium, “Structure, function and diversity of the healthy human microbiome,” Nature, vol. 486, no. 7402, pp. 207–214, 2012. View at Publisher · View at Google Scholar · View at Scopus
  2. J. Qin, R. Li, J. Raes et al., “A human gut microbial gene catalog established by metagenomic sequencing,” Nature, vol. 464, no. 7285, pp. 59–65, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Ramette and P. L. Buttigieg, “A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses,” FEMS Microbiology Ecology, vol. 90, no. 3, pp. 543–550, 2014. View at Publisher · View at Google Scholar · View at Scopus
  4. Human Microbiome Project Consortium, “A framework for human microbiome research,” Nature, vol. 486, no. 7402, pp. 215–221, 2012. View at Publisher · View at Google Scholar · View at Scopus
  5. J. M. Fettweis, J. P. Brooks, M. G. Serrano et al., “Differences in vaginal microbiome in African American women versus women of European ancestry,” Microbiology, vol. 160, Part 10, pp. 2272–2282, 2014. View at Publisher · View at Google Scholar · View at Scopus
  6. R. Plenge, M. Weinblatt, N. Shadick, A. Price, N. Patterson, and D. Reich, “Principal components analysis corrects for stratification in genome-wide association studies,” Nature Genetics, vol. 38, no. 8, pp. 904–909, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. J. Novembre, D. H. Alexander, and K. Lange, “Fast model-based estimation of ancestry in unrelated individuals,” Genome Research, vol. 19, no. 9, pp. 1655–1664, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Novembre, T. Johnson, K. Bryc et al., “Genes mirror geography within Europe,” Nature, vol. 456, no. 7219, p. 274, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. S. P. Lloyd, “Least squares quantization in PCM,” IEEE Transactions on Information Theory, vol. 28, no. 2, pp. 129–137, 1982. View at Publisher · View at Google Scholar · View at Scopus
  10. National Center for Biotechnology Information, 2014, https://www.ncbi.nlm.nih.gov/sra/?term=SRP002462.
  11. P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009, http://aem.asm.org/content/75/23/7537.short?rss=1&ssource=mfc. View at Publisher · View at Google Scholar · View at Scopus
  12. P. D. Schloss, D. Gevers, and S. L. Westcott, “Reducing the effects of PCR amplification and sequencing artifacts on 16s rRNA-based studies,” PLoS One, vol. 6, no. 12, article e27310, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. W. J. Jackson, “2-way cluster assignment,” 2016, https://github.com/westonjackson/2-Way-Cluster-Assignment.