Chuck Merge branch 'master' into compile  over 9 years ago

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@article{deseq,  author = {Love, Michael I M. I.  and Huber, Wolfgang W.  and Anders, Simon}, S.},  title = {{Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2}},  year = {2014},  doi = {10.1101/002832}, 

@article{hoedl_2011,  author = {Hödl, Iris I.  and Hödl, Josef J.  and Wörman, Anders A.  and Singer, Gabriel G.  and Besemer, Katharina K.  and Battin, Tom T.  J.}, journal = {PLoS ONE},  publisher = {Public Library of Science},  title = {{Voronoi tessellation captures very early clustering of single primary cells as induced by interactions in nascent biofilms}}, 

@Manual{vegan,  title = {{vegan: Community Ecology Package}},  author = {Oksanen, Jari J.  and Blanchet, F. Guillaume G.  and Kindt, Roeland R.  and Legendre, Pierre P.  and Minchin, Peter P.  R. and O'Hara, R. B. and Simpson, Gavin G.  L. and Solymos, Peter P.  and Stevens, M. Henry H.  H. and Wagner, Helene}, H.},  year = {2013},  note = {R package version 2.0-10},  }  @article{citeulike:1042553,  author = {Benjamini, Yoav Y.  and Hochberg, Yosef}, Y.},  citeulike-article-id = {1042553},  citeulike-linkout-0 = {http://dx.doi.org/10.2307/2346101},  citeulike-linkout-1 = {http://www.jstor.org/stable/2346101}, 

@article{LANED.J.:1991,  author = {Lane, David D.  J.}, title = {{16S/23S rRNA sequencing}},  journal = {Nucleic Acid Techniques in Bacterial Systematics},  issn = {}, 

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title = {{UCHIME improves sensitivity and speed of chimera detection.}},  date = {2011 Aug 15},  source = {Bioinformatics},  authors = {Edgar, RC R. C.  and Haas, BJ B. J.  and Clemente, JC J. C.  and Quince, C C.  and Knight, R}, R.},  author = {Edgar, RC R. C.  and Haas, BJ B. J.  and Clemente, JC J. C.  and Quince, C C.  and Knight, R}, R.},  year = {2011},  month = {Aug},  jounal = {Bioinformatics}, 

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title = {{An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.}},  date = {2012 Mar},  source = {ISME J},  authors = {McDonald, D D.  and Price, MN M. N.  and Goodrich, J J.  and Nawrocki, EP E. P.  and DeSantis, TZ T. Z.  and Probst, A A.  and Andersen, GL G. L.  and Knight, R R.  and Hugenholtz, P}, P.},  author = {McDonald, D D.  and Price, MN M. N.  and Goodrich, J J.  and Nawrocki, EP E. P.  and DeSantis, TZ T. Z.  and Probst, A A.  and Andersen, GL G. L.  and Knight, R R.  and Hugenholtz, P}, P.},  year = {2012},  month = {},  jounal = {ISME J}, 

title = {{The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.}},  date = {2013 Jan},  source = {Nucleic Acids Res},  authors = {Quast, C and Pruesse, E and Yilmaz, P and Gerken, J and Schweer, T and Yarza, P and Peplies, J and Glöckner, FO},  author = {Quast, C C.  and Pruesse, E E.  and Yilmaz, P P.  and Gerken, J J.  and Schweer, T T.  and Yarza, P P.  and Peplies, J J.  and Glöckner, FO}, F. O.},  year = {2013},  month = {},  jounal = {Nucleic Acids Res}, 

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title = {{Waste not, want not: why rarefying microbiome data is inadmissible.}},  date = {2014 Apr},  source = {PLoS Comput Biol},  authors = {McMurdie, PJ and Holmes, S},  author = {McMurdie, PJ P. J.  and Holmes, S}, year = {2014},  month = {},  jounal = {PLoS Comput Biol}, 

date = {2013 Sep},  source = {Nat Protoc},  authors = {Anders, S and McCarthy, DJ and Chen, Y and Okoniewski, M and Smyth, GK and Huber, W and Robinson, MD},  author = {Anders, S S.  and McCarthy, DJ D. J.  and Chen, Y Y.  and Okoniewski, M M.  and Smyth, GK G. K.  and Huber, W W.  and Robinson, MD}, M. D.},  year = {2013},  month = {},  jounal = {Nat Protoc}, 

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title = {{Architectural differentiation reflects bacterial community structure in stream biofilms.}},  date = {2009 Nov},  source = {ISME J},  authors = {Besemer, K and Hödl, I and Singer, G and Battin, TJ},  author = {Besemer, K K.  and Hödl, I I.  and Singer, G G.  and Battin, TJ}, T. J.},  year = {2009},  month = {},  jounal = {ISME J}, 

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volume = {73},  number = {15},  pages = {4966-4974},  author = {K. Besemer {Besemer, K.  and Singer,  G.Singer  and Limberger,  R.Limberger  and A.-K. Chlup Chlup, A. K.  and Hochedlinger,  G.Hochedlinger  and Hodl,  I.Hodl  and Baranyi,  C.Baranyi  and Battin,  T. J. Battin}, J.},  title = {{Biophysical controls on community succession in stream biofilms}},  journal = {Applied and Environmental Microbiology},  } 

volume = {82},  number = {2},  pages = {555-566},  author = {Colin {Jackson, C.  R.Jackson  and Perry Churchill, P.  F.Churchill  and Eric Roden,  E. Roden}, E.},  title = {{Successional changes in bacterial assemblage structure during epilithic biofilm development}},  journal = {Ecology},  } 

volume = {50},  number = {4},  pages = {589-601},  author = {Emilie Lyautey {Lyautey, E.  and Colin Jackson, C.  R.Jackson  and J\'erôme Cayrou Cayrou, J.  and Jean-Luc Rols Rols, J.  and Fr\'ed\'eric Garab\'etian}, Garab\'etian, F.},  title = {{Bacterial community succession in natural river biofilm assemblages}},  journal = {Microbial Ecology},  }