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Collaborative cloud-enabled tools allow rapid, reproducible biological insights.
Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG. Ragan-Kelley B, et al. Among authors: knight r. ISME J. 2013 Mar;7(3):461-4. doi: 10.1038/ismej.2012.123. Epub 2012 Oct 25. ISME J. 2013. PMID: 23096404 Free PMC article. No abstract available.
Origins of the genetic code: the escaped triplet theory.
Yarus M, Caporaso JG, Knight R. Yarus M, et al. Among authors: knight r. Annu Rev Biochem. 2005;74:179-98. doi: 10.1146/annurev.biochem.74.082803.133119. Annu Rev Biochem. 2005. PMID: 15952885 Review.
PyCogent: a toolkit for making sense from sequence.
Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. Knight R, et al. Genome Biol. 2007;8(8):R171. doi: 10.1186/gb-2007-8-8-r171. Genome Biol. 2007. PMID: 17708774 Free PMC article.
PyNAST: a flexible tool for aligning sequences to a template alignment.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. Caporaso JG, et al. Among authors: knight r. Bioinformatics. 2010 Jan 15;26(2):266-7. doi: 10.1093/bioinformatics/btp636. Epub 2009 Nov 13. Bioinformatics. 2010. PMID: 19914921 Free PMC article.
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. Caporaso JG, et al. Among authors: knight r. Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. Nat Methods. 2010. PMID: 20383131 Free PMC article. No abstract available.
3,327 results