bibliography.bib

%
% List of publications / Leo Lahti.
% http://www.iki.fi/Leo.Lahti/work/pubs/

  @Manual{Caballero_2013,
  title = {df2json: Convert a dataframe to JSON},
  author = {Nacho Caballero},
  year = {2013},
  note = {R package version 0.0.2},
  url = {http://CRAN.R-project.org/package=df2json},
  }

  @Article{Chessel_2004,
  title = {The ade4 package-{I}- {O}ne-table methods},
  author = {D. Chessel and A.B. Dufour and J. Thioulouse},
  journal = {R News},
  year = {2004},
  volume = {4},
  pages = {5-10},
  }

  @Manual{Couture-Beil_2014,
  title = {rjson: JSON for R},
  author = {Alex Couture-Beil},
  year = {2014},
  note = {R package version 0.2.15},
  url = {http://CRAN.R-project.org/package=rjson},
  }

@Manual{Dejean_2014,
  title = {mixOmics: Omics Data Integration Project},
  author = {Sebastien Dejean and Ignacio Gonzalez and Kim-Anh Le Cao with contributions from Pierre Monget and Jeff Coquery and FangZou Yao and Benoit Liquet and Florian Rohart},
  year = {2014},
  note = {R package version 5.0-3},
  url = {http://CRAN.R-project.org/package=mixOmics},
}

@Article{Dray_2007,
  title = {The ade4 package: implementing the duality diagram for ecologists},
  author = {S. Dray and A.B. Dufour},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {22},
  pages = {1-20},
  number = {4},
}

  @Article{Dray_2007a,
  title = {The ade4 package-{II}: {T}wo-table and {K}-table methods.},
  author = {S. Dray and A.B. Dufour and D. Chessel},
  journal = {R News},
  year = {2007},
  volume = {7},
  number = {2},
  pages = {47-52},
  }


@article{HalfvarsonNatMicro,
  author =       {Jonas Halfvarson and Colin J. Brislawn and Regina Lamendella and 
                    Yoshiki Vázquez-Baeza and William A. Walters and Lisa M. Bramer 
                    and Mauro D'Amato and Ferdinando Bonfiglio and Daniel McDonald 
                    and Antonio Gonzalez and Erin E. McClure and Mitchell F. Dunklebarger 
                    and Rob Knight and Janet K. Jansson},
  title =        {Dynamics of the human gut microbiome in inflammatory bowel disease},
  journal =      {{Nature Microbiology}},
  year =         2017,
  volume =       2,
  number =       17004,
  month =        {Feb.},
  doi =          {doi:10.1038/nmicrobiol.2017.4},
  url =          {http://www.nature.com/articles/nmicrobiol20174},
}

@article{Halfvarson_2017,
  title =        {Dynamics of the human gut microbiome in inflammatory bowel disease},
  author = {Jonas Halfvarson and Colin J. Brislawn and Regina Lamendella and 
                    Yoshiki Vázquez-Baeza and William A. Walters and Lisa M. Bramer 
                    and Mauro D'Amato and Ferdinando Bonfiglio and Daniel McDonald 
                    and Antonio Gonzalez and Erin E. McClure and Mitchell F. Dunklebarger 
                    and Rob Knight and Janet K. Jansson},
  journal =      {{Nature Microbiology}},
  year =         {2017},
  volume =       {2},
  month =        {Feb.},
  doi =          {doi:10.1038/nmicrobiol.2017.4},
  url =          {http://www.nature.com/articles/nmicrobiol20174},
}

@article{Lahti11rpa,
  author =       {Leo Lahti and Laura L. Elo and Tero Aittokallio and  
                  Samuel Kaski},
  title =        {Probabilistic Analysis of Probe Reliability in
                  Differential Gene Expression Studies with Short
                  Oligonucleotide Arrays},
  journal =      {{IEEE/ACM Transactions on Computational Biology and
                  Bioinformatics}},
  year =         2011,
  volume =       8,
  number =       1,
  pages =        {217--225},
  month =        {Jan.-Mar.},
  doi =          {doi:10.1109/TCBB.2009.38},
  url =
                  {http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2009.38},
  publisher =    {IEEE Computer Society},
  address =      {Los Alamitos, CA, USA},
  annote =       {Open source implementation:
                  http://bioconductor.org/packages/release/bioc/html/RPA.html}
}

@Article{Lahti13nar,
  author =	 {Leo Lahti and Aurora Torrente and Laura L Elo and
                  Alvis Brazma and Johan Rung},
  title =	 {A fully scalable online pre-processing algorithm for
                  short oligonucleotide microarray atlases},
  journal =	 {Nucleic Acids Research},
  volume =	 41,
  number =	 10,
  year =	 2013,
  pages =	 {e110},
  doi =		 {10.1093/nar/gkt229},
  note =	 {Implementation available through Bioconductor RPA package.}
}

@Article{Lahti13provasI,
  author =	 {Leo Lahti and Anne Salonen and Riina A. Kekkonen and
                  Jarkko Salojarvi and Jonna Jalanka-Tuovinen and Airi
                  Palva and Matej Orešič and Willem M. de Vos},
  title =	 {{Associations between the human intestinal
                  microbiota, {\it Lactobacillus rhamnosus} GG and
                  serum lipids indicated by integrated analysis of
                  high-throughput profiling data}},
  journal =	 {PeerJ},
  year =	 2013,
  volume =	 1,
  pages =	 {e32},
  url =		 {http://dx.doi.org/10.7717/peerj.32},
  pmid =	 23638368
}

  @Article{Lahti_2013,
  title = {A fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases},
  author = {Leo Lahti and Aurora Torrente and Laura L. Elo and Alvis Brazma and Johan Rung},
  journal = {Nucleic Acids Research},
  year = {2013},
  volume = {41},
  issue = {10},
  pages = {e110},
  note = {R/BioC: http://bioconductor.org/packages/release/bioc/html/RPA.html},
  url = {http://nar.oxfordjournals.org/content/41/10/e110},
  }

  @Article{Langfelder_2008,
  author = {Peter Langfelder and Steve Horvath},
  title = {WGCNA: an R package for weighted correlation network analysis},
  journal = {BMC Bioinformatics},
  year = {2008},
  number = {1},
  pages = {559},
  pubmedid = {19114008},
  }
  
@Article{Langfelder_2012,
  title = {Fast {R} Functions for Robust Correlations and Hierarchical Clustering},
  author = {Peter Langfelder and Steve Horvath},
  journal = {Journal of Statistical Software},
  year = {2012},
  volume = {46},
  number = {11},
  pages = {1--17},
  url = {http://www.jstatsoft.org/v46/i11/},
}
  
@Article{McMurdie_2013,
  author = {Paul J. McMurdie and Susan Holmes},
  journal = {PLoS ONE},
  pages = {e61217},
  title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
  volume = {8},
  number = {4},
  year = {2013},
  url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}
  
@Article{Meyer_2008,
  title = {MINET: An open source R/Bioconductor Package for Mutual Information based Network Inference},
  author = {Patrick E. Meyer and Frederic Lafitte and Gianluca Bontempi},
  journal = {BMC Bioinformatics},
  year = {2008},
  volume = {9},
  url = {http://www.biomedcentral.com/1471-2105/9/461},
}
  
@Article{Mullner_2013,
  title = {{fastcluster}: Fast Hierarchical, Agglomerative Clustering Routines for {R} and {Python}},
  author = {Daniel M\"ullner},
  journal = {Journal of Statistical Software},
  year = {2013},
  volume = {53},
  number = {9},
  pages = {1--18},
  url = {http://www.jstatsoft.org/v53/i09/},
  }
  
  @Manual{Oksanen_2015,
  title = {vegan: Community Ecology Package},
  author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
  year = {2015},
  note = {R package version 2.2-1},
  url = {http://CRAN.R-project.org/package=vegan},
}
  
@Manual{Oksanen_2017,
  title = {vegan: Community Ecology Package},
  author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
  year = {2017},
  note = {R package version 2.4-3},
  url = {https://CRAN.R-project.org/package=vegan},
}
  
@Manual{R_Core_Team_2017,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2017},
  url = {https://www.R-project.org/},
}
  
  @Manual{Temple_Lang_2014,
  title = {RCurl: General network (HTTP/FTP/...) client interface for R},
  author = {Duncan {Temple Lang}},
  year = {2014},
  note = {R package version 1.95-4.3},
  url = {http://CRAN.R-project.org/package=RCurl},
  }

@Article{Wickham_2007,
  author = {{Wickham} and {Hadley}},
  journal = {Journal of Statistical Software},
  number = {12},
  title = {Reshaping data with the reshape package},
  url = {http://www.jstatsoft.org/v21/i12/paper},
  volume = {21},
  year = {2007},
}



@Book{Wickham_2009,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2009},
  isbn = {978-0-387-98140-6},
  url = {http://ggplot2.org},
}

@Article{Wickham_2011,
  title = {The Split-Apply-Combine Strategy for Data Analysis},
  author = {Hadley Wickham},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  number = {1},
  pages = {1--29},
  url = {http://www.jstatsoft.org/v40/i01/},
}


@Manual{Wickham_2017,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain Francois and Lionel Henry and Kirill M{\"u}ller},
  year = {2017},
  note = {R package version 0.7.1},
  url = {https://CRAN.R-project.org/package=dplyr},
}



@Manual{Wickham_2017a,
  title = {tidyr: Easily Tidy Data with 'spread()' and 'gather()' Functions},
  author = {Hadley Wickham},
  year = {2017},
  note = {R package version 0.6.3},
  url = {https://CRAN.R-project.org/package=tidyr},
}


@Article{lahti14natcomm,
  author =	 {Leo Lahti and Jarkko Salojarvi and Anne Salonen and
                  Marten Scheffer and Willem M. de Vos},
  title =	 {Tipping elements in the human intestinal ecosystem},
  journal =	 {Nature Communications},
  year =	 2014,
  volume =	 5,
  pages =	 4344,
  month =	 {July},
  doi =		 {10.1038/ncomms5344}
}


@Book{rcore13,
  author = {{R Core Team}},
  title = {R: A language and environment for statistical
    computing},
  publisher = {R Foundation for Statistical Computing},
  year = {2013},
  isbn = {ISBN 3-900051-07-0},
  address = {Vienna, Austria},
  url = {http://www.R-project.org/},
}

@Book{venables02,
  author = {W. N. Venables and B. D. Ripley},
  title = {Modern Applied Statistics with S},
  publisher = {Springer},
  year = {2002},
  isbn = {ISBN },
  address = {New York},
  edition = {fourth},
  isbn = {ISBN },
}