parsimonious.bib

% bmc_article.bib
% 
%  An example of bibtex entries.
%  Entries taken from BMC instructions for authors page.


@article{biscarini2014genome,
	author  = {Biscarini, Filippo and Stevanato, Piergiorgio and Broccanello, Chiara and
                  Stella, Alessandra and Saccomani, Massimo}, 
	title   = {Genome-enabled predictions for binomial traits in
                  sugar beet populations},
	journal = {BMC Genetics},
	year  = 2014, 
	  volume= 18, 
	  number= 5, 
	  pages = {1--9}}	

% Article within a journal
@article{moose2008molecular,
  title={Molecular plant breeding as the foundation for 21st century crop improvement},
  author={Moose, Stephen P and Mumm, Rita H},
  journal={Plant physiology},
  volume=147,
  number=3,
  pages={969--977},
  year=2008,
  publisher={Am Soc Plant Biol}
}
@article{saccomani2009molecular,
  title={Molecular and morpho-physiological characterization of sea, ruderal and cultivated beets},
  author={Saccomani, Massimo and Stevanato, Piergiorgio and Trebbi, Daniele and McGrath, J Mitchell and Biancardi, Enrico},
  journal={Euphytica},
  volume=169,
  number=1,
  pages={19--29},
  year=2009,
  publisher={Springer}
}
@article{stevanato2013high,
  title={High-Throughput RAD-SNP Genotyping for Characterization of Sugar Beet Genotypes},
  author={Stevanato, Piergiorgio and Broccanello, Chiara and Biscarini, Filippo and Del Corvo, Marcello and Sablok, Gaurav and Panella, Lee and Stella, Alessandra and Concheri, Giuseppe},
  journal={Plant Molecular Biology Reporter},
  pages={1--6},
  year=2013,
  publisher={Springer}
}
@article{stevanato2010root,
  title={Root traits and yield in sugar beet: identification of AFLP markers associated with root elongation rate},
  author={Stevanato, Piergiorgio and Trebbi, Daniele and Saccomani, Massimo},
  journal={Euphytica},
  volume=173,
  number=3,
  pages={289--298},
  year=2010,
  publisher={Springer}
}
@article{chaitin2006limits,
  title={The limits of reason},
  author={Chaitin, Gregory},
  journal={Scientific American},
  volume={294},
  number={3},
  pages={74--81},
  year={2006},
  publisher={Nature Publishing Group}
}
@article{meuwissen2001prediction,
  title={Prediction of total genetic value using genome-wide dense marker maps},
  author={Meuwissen, THE and Hayes, BJ and Goddard},
  journal={Genetics},
  volume=157,
  number=4,
  pages={1819--1829},
  year=2001,
  publisher={Genetics Soc America}
}
@article{wurschum2013genomic,
  title={Genomic selection in sugar beet breeding populations},
  author={W{\"u}rschum, Tobias and Reif, Jochen C and Kraft, Thomas and Janssen, Geert and Zhao, Yusheng},
  journal={BMC genetics},
  volume=14,
  number=1,
  pages=85,
  year=2013,
  publisher={BioMed Central Ltd}
}
@article{hofheinz2012genome,
  title={Genome-based prediction of test cross performance in two subsequent breeding cycles},
  author={Hofheinz, Nina and Borchardt, Dietrich and Weissleder, Knuth and Frisch, Matthias},
  journal={Theoretical and Applied Genetics},
  volume=125,
  number=8,
  pages={1639--1645},
  year=2012,
  publisher={Springer}
}	
@article{heffner2010plant,
  title={Plant breeding with genomic selection: gain per unit time and cost},
  author={Heffner, Elliot L and Lorenz, Aaron J and Jannink, Jean-Luc and Sorrells, Mark E},
  journal={Crop science},
  volume=50,
  number=5,
  pages={1681--1690},
  year=2010,
  publisher={Crop Science Society of America}
}
@article{goddard2007genomic,
  title={Genomic selection},
  author={Goddard, ME and Hayes, BJ},
  journal={Journal of Animal Breeding and Genetics},
  volume=124,
  number=6,
  pages={323--330},
  year=2007,
  publisher={Wiley Online Library}
}
@article{dohm2013genome,
  title={The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)},
  author={Dohm, Juliane C and Minoche, Andr{\'e} E and Holtgr{\"a}we, Daniela and Capella-Guti{\'e}rrez, Salvador and Zakrzewski, Falk and Tafer, Hakim and Rupp, Oliver and S{\"o}rensen, Thomas Rosleff and Stracke, Ralf and Reinhardt, Richard and others},
  journal={Nature},
  year=2013,
  publisher={Nature Publishing Group}
}
@article{jonas2013does,
  title={Does genomic selection have a future in plant breeding?},
  author={Jonas, Elisabeth and de Koning, Dirk-Jan},
  journal={Trends in biotechnology},
  volume=31,
  number=9,
  pages={497--504},
  year=2013,
  publisher={Elsevier}
}
@article{hall2009weka,
  title={The WEKA data mining software: an update},
  author={Hall, Mark and Frank, Eibe and Holmes, Geoffrey and Pfahringer, Bernhard and Reutemann, Peter and Witten, Ian H},
  journal={ACM SIGKDD explorations newsletter},
  volume={11},
  number={1},
  pages={10--18},
  year={2009},
  publisher={ACM}
}
@article{dimauro2013use,
  title={Use of the canonical discriminant analysis to select SNP markers for bovine breed assignment and traceability purposes},
  author={Dimauro, Corrado and Cellesi, Massimo and Steri, Roberto and Gaspa, Giustino and Sorbolini, Silvia and Stella, Alessandra and Macciotta, Nicol{\`o} Pietro Paolo},
  journal={Animal genetics},
  volume=44,
  number=4,
  pages={377--382},
  year=2013,
  publisher={Wiley Online Library}
}
@article{schuster2007next,
  title={Next-generation sequencing transforms today’s biology},
  author={Schuster, Stephan C},
  journal={Nature},
  volume=200,
  number=8,
  year=2007
}
@article{elshire2011robust,
  title={A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species},
  author={Elshire, Robert J and Glaubitz, Jeffrey C and Sun, Qi and Poland, Jesse A and Kawamoto, Ken and Buckler, Edward S and Mitchell, Sharon E},
  journal={PloS one},
  volume=6,
  number=5,
  pages={e19379},
  year=2011,
  publisher={Public Library of Science}
}
@article{oliphant2002beadarray,
  title={BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping},
  author={Oliphant, Arnold and Barker, David L and Stuelpnagel, John R and Chee, Mark S},
  journal={Biotechniques},
  volume=32,
  number=6,
  pages={56--58},
  year=2009
}
@article{natbiotechnol2009genome,
 title={The genome-assisted barnyard},
 author={Nat. Biotechnol., Editor},
 journal={Nature Biotechnology},
 volume=27,
 pages={487},
 year=2009
}
@article{zhang2012progress,
  title={Progress of genome wide association study in domestic animals},
  author={Zhang, Hui and Wang, Zhipeng and Wang, Shouzhi and Li, Hui},
  journal={J Anim Sci Biotech},
  volume=3,
  pages=26,
  year=2012
}
@article{cole2012breeding,
  title={BREEDING AND GENETICS SYMPOSIUM: Really big data: Processing and analysis of very large data sets},
  author={Cole, JB and Newman, S and Foertter, F and Aguilar, I and Coffey, M},
  journal={Journal of Animal Science},
  volume={90},
  number={3},
  pages={723--733},
  year={2012},
  publisher={American Society of Animal Science}
}
@article{salah2012genetic,
  title={Genetic identification of a novel bolting locus in \emph{Beta
                  vulgaris} which promotes annuality independently of
                  the bolting gene \emph{B}},
  author={Abou-Elwafa, SF and B\"{u}ttner, B and Kopisch-Obuch, FJ and
                  Jung, C and M\"{u}ller, AE},
  journal={Molecular Breeding},
  volume=29,
  pages={989--998},
  year=2012,
  publisher={Elsevier}
}
@article{russu2012stochastic,
  title={Stochastic model search with binary outcomes for genome-wide association studies},
  author={Russu, Alberto and Malovini, Alberto and Puca, Annibale A and Bellazzi, Riccardo},
  journal={Journal of the American Medical Informatics Association},
  volume=19,
  number={e1},
  pages={e13--e20},
  year=2012,
  publisher={BMJ Publishing Group Ltd}
}
@article{goddard2009mapping,
  title={Mapping genes for complex traits in domestic animals and their use in breeding programmes},
  author={Goddard, Michael E and Hayes, Ben J},
  journal={Nature Reviews Genetics},
  volume=10,
  number=6,
  pages={381--391},
  year=2009,
  publisher={Nature Publishing Group}
}
@inproceedings{pirola2013haplotype,
  title={Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes},
  author={Pirola, Yuri and Vedova, Gianluca Della and Bonizzoni, Paola and Stella, Alessandra and Biscarini, Filippo},
  booktitle={Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics},
  pages=33,
  year=2013,
  organization={ACM}
}
@article{pacheco2011convenient,
  title={Convenient genotyping of nine bovine K-casein variants},
  author={Pacheco Contreras, V{\'\i}ctor I and Lourenco Jaramillo, Diana L and Parra Bracamonte, Gaspar M and Mart{\'\i}nez Gonz{\'a}lez, Juan C and Sifuentes Rinc{\'o}n, Ana M},
  journal={Electronic Journal of Biotechnology},
  volume=14,
  number=4,
  pages={12--12},
  year=2011,
  publisher={SciELO Chile}
}
@article{browning2007rapid,
  title={Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering},
  author={Browning, Sharon R and Browning, Brian L},
  journal={The American Journal of Human Genetics},
  volume=81,
  number=5,
  pages={1084--1097},
  year=2007,
  publisher={Elsevier}
}
@article{browning2006multilocus,
  title={Multilocus association mapping using variable-length Markov chains},
  author={Browning, Sharon R},
  journal={The American Journal of Human Genetics},
  volume=78,
  number=6,
  pages={903--913},
  year=2006,
  publisher={Elsevier}
}
@article{bohmanova2010characteristics,
  title={Characteristics of linkage disequilibrium in North American Holsteins},
  author={Bohmanova, Jarmila and Sargolzaei, Mehdi and Schenkel, Flavio S},
  journal={BMC genomics},
  volume=11,
  number=1,
  pages=421,
  year=2010,
  publisher={BioMed Central Ltd}
}
@article{gianola2009additive,
  title={Additive genetic variability and the Bayesian alphabet},
  author={Gianola, Daniel and de Los Campos, Gustavo and Hill, William G and Manfredi, Eduardo and Fernando, Rohan},
  journal={Genetics},
  volume=183,
  number=1,
  pages={347--363},
  year=2009,
  publisher={Genetics Soc America}
}
@article{liu2011multilocus,
  title={Multilocus association mapping using generalized ridge logistic regression},
  author={Liu, Zhe and Shen, Yuanyuan and Ott, Jurg},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={384},
  year={2011},
  publisher={BioMed Central Ltd}
}
@article{fawcett2004roc,
  title={ROC graphs: Notes and practical considerations for researchers},
  author={Fawcett, Tom},
  journal={Machine learning},
  volume=31,
  pages={1--38},
  year=2004
}

% Article within a journal supplement
@ARTICLE{oreg,
	author  = {Orengo, C A and Bray, J E and Hubbard, 
		   T and LoConte, L and Sillitoe, I}, 
	title   = {Analysis and assessment of ab initio 
		   three-dimensional prediction, secondary 
		   structure, and contacts prediction},
	journal = {Proteins}, 
	year    = {1999},
	volume  = {Suppl 3}, 
	pages   = {149-170}
}	

% In press article
@inpress{khar,
	author  = {Kharitonov, S A and Barnes, P J}, 
	title   = {Clinical aspects of exhaled nitric oxide},
	journal = {Eur Respir J}, 
	note    = {in press} 
}	

%
% Published abstract
%
@ARTICLE{zvai,
	author  = {Zvaifler, N J and Burger, J A and Marinova-Mutafchieva, 
		   L and Taylor, P and Maini, R N},
	title   = {Mesenchymal cells, stromal derived factor-1 and 
		   rheumatoid arthritis [abstract]},
	journal = {Arthritis Rheum}, 
	year    = {1999},
	volume  = {42}, 
	pages   = {s250},
}	


%
% Article within conference proceedings
%
@Inproceedings{schwarzenbacher2012genome,
	author    = {Schwarzenbacher, H and F\"{u}rst, C and F\"{u}rst-Waltl, B and Dolezal, M}, 
	title     = {A genome-wide search for harmful recessive haplotypes in Brown Swiss and Fleckvieh cattle},
	booktitle = {Book of Abstracts of the $63^{rd}$ EAAP Annual
                  Meeting, Bratislava},
	year      = 2012,
	  editor  = {EAAP}, 
	  pages   = 171
}	

@Inproceedings{bacciu2012linkage,
	author    = {Bacciu, N and Bomba, L and Nicolazzi, E L and
                  Milanesi, M and Ajmone-Marsan, P}, 
	title     = {Linkage disequilibrium in {BTA6} for the italian holstein breed using
  a 54k and 800k {SNP}-chip},
	booktitle = {Proceedings of the 16th QTL-MAS workshop, Alghero - Italy},
	year      = 2012
}	

%%%%%%%%
%  Book chapter, or article within a book
%
@incollection{hastie2009model,
	author    = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome}, 
        title = {Model Assessment and Selection},
	booktitle     = {The elements of statistical learning},
	publisher = {Springer}, 
	year      = {2009},
        pages = {219--260},
	address   = {New York, NY, USA} 
}
@incollection{james2013moving,
	author    = {James, G and Witten, D and Hastie, T and
                  Tibshirani, R}, 
        title = {Moving beyond linearity},
	booktitle     = {An introduction to statistical learning - with
                  applications in R},
	publisher = {Springer}, 
	year      = {2013},
        pages = {208-209},
	address   = {} 
}

@incollection{schn,
	author    = {E Schnepf}, 
	title     = {From prey via endosymbiont to plastids: 
		     comparative studies in dinoflagellates},
	booktitle = {Origins of Plastids}, 
	editor    = {R A Lewin}, 
	publisher = {Chapman and Hall},
	pages     = {53-76}, 
	year      = {1993},
	  address = {New York}, 
	  volume  = {2}, 
	  edition = {2nd} 
}	
@incollection{james2013,
	author    = {James, G and Witten, D and Hastie, T and
                  Tibshirani, R}, 
        title = {Linear Model Selection and Regularization},
	booktitle     = {An introduction to statistical learning - with
                  applications in R},
	publisher = {Springer}, 
	year      = {2013},
        pages = {208-209},
	address   = {} 
}


%%%%%%%%
% Whole issue of journal
%
@wholejournal{pond,
	editor  = {B Ponder and S Johnston and L Chodosh}, 
	title   = {Innovative oncology},
	journal = {Breast Cancer Res}, 
	year  = {1998},
	  volume= {10}, 
	  pages = {1-72}
}	


%%%%%%%%
% Whole conference proceedings
%
@proceedings{smith,
	editor  = {Y Smith}, 
	title   = {Proceedings of the First National Conference
		   on Porous Sieves: 27-30 June 1996; Baltimore},
	year = 1996,
	  address= {Stoneham}, 
	  publisher = {Butterworth-Heinemann},
}	


%%%%%%%%
% Complete book
%
@book{mardia2000,
	author    = {Mardia, K V and Kent, J T and Bibby, J M}, 
	title     = {Multivariate Analysis},
	publisher = {Academic Press}, 
	year      = {2000},
	address   = {London} 
}
@book{MATLAB2010,
year = {2010},
author = {MATLAB},
title = {version 7.10.0 (R2010a)},
publisher = {The MathWorks Inc.},
address = {Natick, Massachusetts}
}
%%%%%%%%
% Monograph or book in series 
%
@incollection{hunn,
	author    = {G W Hunninghake and J E Gadek}, 
	title     = {The alveloar macrophage},
	booktitle = {Cultured Human Cells and Tissues},
	publisher = {Academic Press}, 
	year      = {1995},
  pages      = {54-56},
	  editor   = {T J R Harris}, 
	  address  = {New York}, 
	  note     = {Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1} 
}


%%%%%%%%
% Book with institutional author
@Manual{r2008manual,
     title = {R: A Language and Environment for Statistical Computing},
     author = {{R Development Core Team}},
     organization = {R Foundation for Statistical Computing},
     address = {Vienna, Austria},
     year = 2008,
     note = {{ISBN} 3-900051-07-0},
     url = {http://www.R-project.org},
   }


%%%%%%%%
% PHD Thesis
%
@phdthesis{koha,
	author = {R Kohavi}, 
	title  = {Wrappers for performance enhancement and
		  obvious decision graphs},
	school = {Stanford University, Computer Science Department},
	year   = {1995}
}

%%%%%%%%
% Webpage Link / URL
%
@webpage{gnumeric2014,
	title  = {The Gnumeric Spreadsheet},
	url = {http://www.gnumeric.org/},
        year=2014,
        author={GNOME-Project}
}