Morgan, X.C. et al. Genome Biol. 13, R79 (2012).
Ravel, J. et al. Proc. Natl. Acad. Sci. USA 108 (suppl. 1), 4680–4687 (2011).
Qin, J. et al. Nature 490, 55–60 (2012).
Harris, J.K. & Wagner, B.D. J. Allergy Clin. Immunol. 129, 441–442 (2012).
Turnbaugh, P.J. et al. Nature 457, 480–484 (2009).
Scher, J.U. et al. Arthritis Rheum. 64, 3083–3094 (2012).
Caporaso, J.G. et al. Nat. Methods 7, 335–336 (2010).
Lozupone, C. & Knight, R. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Ghodsi, M., Liu, B. & Pop, M. BMC Bioinformatics 12, 271 (2011).
Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Rodriguez-Brito, B., Rohwer, F. & Edwards, R.A. BMC Bioinformatics 7, 162 (2006).
White, J.R., Nagarajan, N. & Pop, M. PLoS Comput. Biol. 5, e1000352 (2009).
Segata, N. et al. Genome Biol. 12, R60 (2011).
Bullard, J.H., Purdom, E., Hansen, K.D. & Dudoit, S. BMC Bioinformatics 11, 94 (2010).
Dillies, M.A. et al. Brief. Bioinform. 10.1093/bib/bbs046 (17 September 2012).
Turnbaugh, P.J. et al. Sci. Transl. Med. 1, 6ra14 (2009).
Anders, S. & Huber, W. Genome Biol. 11, R106 (2010).
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. Bioinformatics 26, 139–140 (2010).
White, J.R. et al. BMC Bioinformatics 11, 152 (2010).
Friedman, J. & Alm, E.J. PLoS Comput. Biol. 8, e1002687 (2012).
Faust, K. et al. PLoS Comput. Biol. 8, e1002606 (2012).
The Human Microbiome Project Consortium. Nature 486, 215–221 (2012).
Smyth, G.K. in Bioinformatics and Computational Biology Solutions using R and Bioconductor (eds. Gentleman, R., Carey, V., Huber, W., Irizarry, R. & Dudoit, S.) 397–420 (Springer, 2005).
Langendijk-Genevaux, P.S., Grimm, W.D. & van der Hoeven, J.S. J. Clin. Periodontol. 28, 1151–1157 (2001).
Segata, N. et al. Genome Biol. 13, R42 (2012).
Paster, B.J. et al. J. Bacteriol. 183, 3770–3783 (2001).
Colombo, A.P. et al. J. Periodontol. 80, 1421–1432 (2009).
Langmead, B., Hansen, K.D. & Leek, J.T. Genome Biol. 11, R83 (2010).
Charlson, E.S. et al. Am. J. Respir. Crit. Care Med. 184, 957–963 (2011).
Frazee, A.C., Langmead, B. & Leek, J.T. BMC Bioinformatics 12, 449 (2011).
