To cite the original statistical method and normalization method
implemented in metagenomeSeq use

  Paulson JN, Stine OC, Bravo HC, Pop M (2013). “Differential abundance
  analysis for microbial marker-gene surveys.” _Nat Meth_, *advance
  online publication*. doi:10.1038/nmeth.2658
  <https://doi.org/10.1038/nmeth.2658>,
  <http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Differential abundance analysis for microbial marker-gene surveys},
    author = {Joseph N. Paulson and Oscar Colin Stine and Hector Corrada Bravo and Mihai Pop},
    year = {2013},
    journal = {Nat Meth},
    volume = {advance online publication},
    doi = {10.1038/nmeth.2658},
    url = {http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html},
  }

To cite the metagenomeSeq software/vignette guide use

  Paulson JN, Olson ND, Braccia DJ, Wagner J, Talukder H, Pop M, Bravo
  HC (2013). _metagenomeSeq: Statistical analysis for sparse
  high-throughput sequncing._. Bioconductor package,
  <http://www.cbcb.umd.edu/software/metagenomeSeq>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {metagenomeSeq: Statistical analysis for sparse high-throughput sequncing.},
    author = {Joseph N. Paulson and Nathan D. Olson and Domenick J. Braccia and Justin Wagner and Hisham Talukder and Mihai Pop and Hector Corrada Bravo},
    year = {2013},
    note = {Bioconductor package},
    url = {http://www.cbcb.umd.edu/software/metagenomeSeq},
  }

To cite time series analysis/function fitTimeSeries use

  Paulson* JN, Talukder* H, Bravo HC (2017). “Longitudinal differential
  abundance analysis of marker-gene surveys using smoothing splines.”
  _biorxiv_. doi:10.1101/099457 <https://doi.org/10.1101/099457>,
  <https://www.biorxiv.org/content/10.1101/099457v1>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Longitudinal differential abundance analysis of marker-gene surveys using smoothing splines},
    author = {Joseph N. Paulson* and Hisham Talukder* and Hector Corrada Bravo},
    year = {2017},
    journal = {biorxiv},
    doi = {10.1101/099457},
    url = {https://www.biorxiv.org/content/10.1101/099457v1},
  }