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paper.bib
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@article{caporaso2010qiime,
author = "J Gregory Caporaso and Justin Kuczynski and Jesse Stombaugh and Kyle Bittinger and Frederic D Bushman and Elizabeth K Costello and Noah Fierer and Antonio Gonzalez Pena and Julia K Goodrich and Jeffrey I Gordon and Gavin A Huttley and Scott T Kelley and Dan Knights and Jeremy E Koenig and Ruth E Ley and Catherine A Lozupone and Daniel McDonald and Brian D Muegge and Meg Pirrung and Jens Reeder and Joel R Sevinsky and Peter J Turnbaugh and William A Walters and Jeremy Widmann and Tanya Yatsunenko and Jesse Zaneveld and Rob Knight",
title = "QIIME allows analysis of high-throughput community sequencing data",
journal = "Nature Methods",
volume = "7",
number = "5",
pages = "335–336",
year = 2010,
url = "http://doi.org/10.1038/nmeth.f.303"
}
@article{de2009associations,
author = "Cáceres, M. De and Legendre, P.",
title = "Associations between species and groups of sites: indices and statistical inference",
journal = "Ecology",
volume = "90",
number = "12",
pages = "3566–3574",
year = 2009,
url = "http://doi.org/10.1890/08-1823.1"
}
@article{love2014moderated,
author = "Love, M. I. and Huber, W. and Anders, S.",
title = "Moderated estimation of fold change and dispersion for {RNA}-seq data with {DESeq}2",
journal = "Genome Biology",
volume = "15",
number = "12",
pages = "550",
year = 2014,
url = "http://doi.org/10.1186/s13059-014-0550-8"
}
@article{mandal2015analysis,
author = "Mandal, S. and Van Treuren and W., White and R. A. and Eggesbø, M. and Knight, R. and Peddada, S. D.",
title = "Analysis of composition of microbiomes: a novel method for studying microbial composition",
journal = "Microbial Ecology in Health and Disease",
volume = "26",
pages = "27663",
year = 2015,
url = "http://doi.org/10.3402/mehd.v26.27663"
}
@article{mcmurdie2013phyloseq,
author = "McMurdie, P. J. and Holmes, S.",
title = "phyloseq: an {R} package for reproducible interactive analysis and graphics of microbiome census data",
journal = "PloS One",
volume = "8",
number = "4",
pages = "e61217",
year = 2013,
url = "http://doi.org/10.1371/journal.pone.0061217"
}
@article{paulson2013differential,
author = "Paulson, J. N. and Stine, O. C. and Bravo, H. C. and Pop, M.",
title = "Differential abundance analysis for microbial marker-gene surveys",
journal = "Nature Methods",
volume = "10",
number = "12",
pages = "1200-1202",
year = 2013,
url = "http://doi.org/10.1038/nmeth.2658"
}