
%% NOTE
%% Need to check whether journal abbreviations are needed for BMC format
%% DONE - Should be abbreviated now 


@Article{Alv2007,
   author = {Gregory Alvord, W. and Roayaei, J. A. and Quinones, O. A. and Schneider, K. T.}, 
   title = {A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R},
   journal = {Brief Bioinform},
   volume = {8},
   number = {6},
   pages = {415-31},
   year = {2007}
}

@Article{Barg2010,
   author = {Bargaje, R. and Hariharan, M. and Scaria, V. and Pillai, B.},
   title = {Consensus mi{RNA} expression profiles derived from interplatform normalization of microarray data},
   journal = {RNA},
   volume = {16},
   number = {1},
   pages = {16-25},
   year=2010,
}

@Article{Bart2009,
   author = {Bartel, D. P.},
   title = {Micro{RNA}s: target recognition and regulatory functions},
   journal = {Cell},
   volume = {136},
   number = {2},
   pages = {215-33},
   year = {2009}
}

@Article{Ben1995, 
  author = {Benjamini, Y. and Hochberg, Y.}, 
  title  = {Controlling the false discovery rate: a practical and powerful approach to multiple testing}, 
  journal = {J R Stat Soc Series B Stat Methodol}, 
  volume = {57}, 
  pages = {289-300},	
  year = {1995}
}


@Article{Bro2008, 
  author = {Brock, G.N. and Pihur, V. and Datta, S. and Datta, S.},
  title  = {\pkg{clValid}, an {R} package for cluster  validation},
  journal = {J Stat Softw}, 
  volume = {25}, 
  issue = {4}, 
  year = {2008}
}

@Article{Cor2007,
   author = {Corney, D. C. and Flesken-Nikitin, A. and Godwin, A. K. and Wang, W. and Nikitin, A. Y.},
   title = {Micro{RNA}-34b and Micro{RNA}-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth},
   journal = {Cancer Res},
   volume = {67},
   number = {18},
   pages = {8433-8},
   year = {2007}
}

@article{Dop1997,
  Author={Dopazo, J. and Carazo, J. M.},
  Title={Phylogenetic reconstruction using a growing neural network that adopts the topology of a phylogenetic tree},
  Journal={Journal of Molecular Evolution},
  Year={1997},
  Volumen={44},
  Pages={226-233}
}


@Article{Efron2001, 
   author = {Efron, B. and Tibshirani, R. and Storey, J. D. and Tusher V.}, 
   title = {Empirical Bayes analysis of a microarray experiment}, 
   journal = {Journal of the American Statistical Association}, 
   volume = {96},
   pages = {1151-1160},
   year = {2001}
}

@Article{Fer2009,
   author = {Ferretti, E. and De Smaele, E. and Po, A. and Di Marcotullio, L. and Tosi, E. and Espinola, M. S. and Di Rocco, C. and Riccardi, R. and Giangaspero, F. and Farcomeni, A. and Nofroni, I. and Laneve, P. and Gioia, U. and Caffarelli, E. and Bozzoni, I. and Screpanti, I. and Gulino, A.},
   title = {Micro{RNA} profiling in human medulloblastoma},
   journal = {Int J Cancer},
   volume = {124},
   number = {3},
   pages = {568-77},
   year = {2009}
}

@article{Fra2001,
  Author={Fraley, C. and Raftery, A. E.},
  Title={Model-based clustering, discriminant analysis, and density estimation},
  Journal={J Am Stat Assoc}, 
  Year={2001},
  Volume={17},
  Pages={126-136}
}

%% Bioconductor 
@Article{Gen2004,
    author = {Robert C Gentleman and Vincent J. Carey and Douglas M. Bates and {others}},
    title = {Bioconductor: Open software development for computational biology and bioinformatics},
    journal = {Genome Biol},
    volume = {5},
    year = {2004},
    pages = {R80}
}
%%     url = {http://genomebiology.com/2004/5/10/R80},


@Article{Gen2005,
   author = {Gentleman, R.},
   title = {Reproducible research: a bioinformatics case study},
   journal = {Stat Appl Genet Mol Biol},
   volume = {4},
   pages = {Article2},
   year = {2005}
}

@Article{Got2007,
   author = {Gottardo, F. and Liu, C. G. and Ferracin, M. and Calin, G. A. and Fassan, M. and Bassi, P. and Sevignani, C. and Byrne, D. and Negrini, M. and Pagano, F. and Gomella, L. G. and Croce, C. M. and Baffa, R.},
   title = {Micro-{RNA} profiling in kidney and bladder cancers},
   journal = {Urol Oncol},
   volume = {25},
   number = {5},
   pages = {387-92},
   year = {2007}
}

@Article{Gri2008,
   author = {Griffiths-Jones, S. and Saini, H. K. and van Dongen, S. and Enright, A. J.},
   title = {miRBase: tools for micro{RNA} genomics},
   journal = {Nucleic Acids Res},
   volume = {36},
   number = {Database issue},
   pages = {D154-8},
   year = {2008}
}


@article{Har1979,
  Author={Hartigan, J. A. and Wong, M. A.},
  Title={A k-means clustering algorithm},
  Journal={Applied Statistics},
  Year={1979},
  Volume={28},
  Pages={100-108}
}


@Article{Hicks2008,
   author = {Hicks, J. A. and Tembhurne, P. and Liu, H. C.},
   title = {Micro{RNA} expression in chicken embryos},
   journal = {Poult Sci},
   volume = {87},
   number = {11},
   pages = {2335-43},
   year = {2008}
}


@Article{Hua2008,
   author = {Hua, Y. J. and Tu, K. and Tang, Z. Y. and Li, Y. X. and Xiao, H. S.},
   title = {Comparison of normalization methods with micro{RNA} microarray},
   journal = {Genomics},
   volume = {92},
   number = {2},
   pages = {122-8},
   year = {2008}
}

@Article{Hub2002,
 author = {Huber, W. and von Heydebreck, A. and Sultmann, H. and Poustka, A. and Vingron, M.},
   title = {Variance stabilization applied to microarray data calibration and to the quantification of differential expression},
   journal = {Bioinformatics},
   volume = {18 Suppl 1},
   pages = {S96-104},
   year = {2002}
}


@Article{Ibb2009,
   author = {Ibberson, D. and Benes, V. and Muckenthaler, M. U. and Castoldi, M.},
   title = {{RNA} degradation compromises the reliability of micro{RNA} expression profiling},
   journal = {BMC Biotechnol},
   volume = {9},
   pages = {102},
   year = {2009}
}

@book{Kau1990,
  Author={Kaufman, L. and Rousseeuw, P. J.},
  Title={Finding Groups in Data. An Introduction to Cluster Analysis},
  Publisher={Wiley},
  Year={1990},
  address={New York}
}


@Article{Kauf2009,
   author = {Kauffmann, A. and Gentleman, R. and Huber, W.},
   title = {arrayQualityMetrics--a bioconductor package for quality assessment of microarray data},
   journal = {Bioinformatics},
   volume = {25},
   number = {3},
   pages = {415-6},
   year = {2009}
}

@Article{Kau2010,
   author = {Kauffmann, A. and Huber, W.},
   title = {Microarray data quality control improves the detection of differentially expressed genes},
   journal = {Genomics},
   volume = {95},
   number = {3},
   pages = {138-42},
   year = 2010,
}

@book{Koh1997,
  Author={Kohonen, T.},
  Title={Self-Organizing Maps},
  Edition={2nd},
  Publisher={Springer-Verlag},
  Year={1997}
}

@Article{Kong2009,
   author = {Kong, W. and Zhao, J. J. and He, L. and Cheng, J. Q.},
   title = {Strategies for profiling micro{RNA} expression},
   journal = {J Cell Physiol},
   volume = {218},
   number = {1},
   pages = {22-5},
   year = {2009}
}

@Article{Kren2009,
   author = {Kren, B. T. and Wong, P. Y. and Sarver, A. and Zhang, X. and Zeng, Y. and Steer, C. J.},
   title = {Micro{RNA}s identified in highly purified liver-derived mitochondria may play a role in apoptosis},
   journal = {RNA Biol},
   volume = {6},
   number = {1},
   pages = {65-72},
   year = {2009}
}

@Article{Lak2007,
   author = {Lakshmipathy, U. and Love, B. and Goff, L. A. and Jornsten, R. and Graichen, R. and Hart, R. P. and Chesnut, J. D.},
   title = {Micro{RNA} expression pattern of undifferentiated and differentiated human embryonic stem cells},
   journal = {Stem Cells Dev},
   volume = {16},
   number = {6},
   pages = {1003-16},
   year = {2007}
}


@Article{Land2007,
   author = {Landgraf, P. and Rusu, M. and Sheridan, R. and Sewer, A. and Iovino, N. and Aravin, A. and Pfeffer, S. and Rice, A. and Kamphorst, A. O. and Landthaler, M. and Lin, C. and Socci, N. D. and Hermida, L. and Fulci, V. and Chiaretti, S. and Foa, R. and Schliwka, J. and Fuchs, U. and Novosel, A. and Muller, R. U. and Schermer, B. and Bissels, U. and Inman, J. and Phan, Q. and Chien, M. and Weir, D. B. and Choksi, R. and De Vita, G. and Frezzetti, D. and Trompeter, H. I. and Hornung, V. and Teng, G. and Hartmann, G. and Palkovits, M. and Di Lauro, R. and Wernet, P. and Macino, G. and Rogler, C. E. and Nagle, J. W. and Ju, J. and Papavasiliou, F. N. and Benzing, T. and Lichter, P. and Tam, W. and Brownstein, M. J. and Bosio, A. and Borkhardt, A. and Russo, J. J. and Sander, C. and Zavolan, M. and Tuschl, T.},
   title = {A mammalian micro{RNA} expression atlas based on small {RNA} library sequencing},
   journal = {Cell},
   volume = {129},
   number = {7},
   pages = {1401-14},
   year = {2007}
}

@Article{Li2009,
   author = {Li, W. and Ruan, K.},
   title = {Micro{RNA} detection by microarray},
   journal = {Anal Bioanal Chem},
   volume = {394},
   number = {4},
   pages = {1117-24},
   year = {2009}
}

@Article{Liu2008a,
   author = {Liu, C. G. and Calin, G. A. and Volinia, S. and Croce, C. M.},
   title = {Micro{RNA} expression profiling using microarrays},
   journal = {Nat Protoc},
   volume = {3},
   number = {4},
   pages = {563-78},
   year = {2008}
}

@Article{Liu2008b,
   author = {Liu, C. G. and Spizzo, R. and Calin, G. A. and Croce, C. M.},
   title = {Expression profiling of micro{RNA} using oligo DNA arrays},
   journal = {Methods},
   volume = {44},
   number = {1},
   pages = {22-30},
   year = {2008}
}

@Article{Muk2010,
    author = {Mukhopadhyay, P. and Brock, G. and Pihur, V. and Webb, C. and Pisano, M. M. and Greene, R. M.},
   title = {Developmental micro{RNA} expression profiling of murine embryonic orofacial tissue},
   journal = {Birth Defects Res A Clin Mol Teratol},
   volume = {88},
   number = {7},
   pages = {511-34},
   year = {2010}
}

@Article{Oh2010, 
 author = {Oh, S. and Kang, D. D. and Brock, G. N. and Tseng, G. C.},
   title = {Biological impact of missing-value imputation on downstream analyses of gene expression profiles},
   journal = {Bioinformatics},
   volume = {27},
   number = {1},
   pages = {78-86},
   year = {2010}
}


@Article{Pra2009,
   author = {Pradervand, S. and Weber, J. and Thomas, J. and Bueno, M. and Wirapati, P. and Lefort, K. and Dotto, G. P. and Harshman, K.},
   title = {Impact of normalization on mi{RNA} microarray expression profiling},
   journal = {RNA},
   volume = {15},
   number = {3},
   pages = {493-501},
   year = {2009}
}

@Article{Rao2008,
   author = {Rao, Y. and Lee, Y. and Jarjoura, D. and Ruppert, A. S. and Liu, C. G. and Hsu, J. C. and Hagan, J. P.},
   title = {A comparison of normalization techniques for micro{RNA} microarray data},
   journal = {Stat Appl Genet Mol Biol},
   volume = {7},
   number = {1},
   pages = {Article22},
   year = {2008}
}

@Article{Ris2009,
   author = {Risso, D. and Massa, M. S. and Chiogna, M. and Romualdi, C.},
   title = {A modified LOESS normalization applied to micro{RNA} arrays: a comparative evaluation},
   journal = {Bioinformatics},
   volume = {25},
   number = {20},
   pages = {2685-91},
   year = {2009}
}

@Article{Rit2006,
   author = {Ritchie, M. E. and Diyagama, D. and Neilson, J. and van Laar, R. and Dobrovic, A. and Holloway, A. and Smyth, G. K.},
   title = {Empirical array quality weights in the analysis of microarray data},
   journal = {BMC Bioinformatics},
   volume = {7},
   pages = {261},
   year = {2006}
}

@Article{Rit2007,
   author = {Ritchie, M. E. and Silver, J. and Oshlack, A. and Holmes, M. and Diyagama, D. and Holloway, A. and Smyth, G. K.},
   title = {A comparison of background correction methods for two-colour microarrays},
   journal = {Bioinformatics},
   volume = {23},
   number = {20},
   pages = {2700-7},
   year = {2007}
}

@Article{Rus2004,
   author = {Ruschhaupt, M. and Huber, W. and Poustka, A. and Mansmann, U.},
   title = {A compendium to ensure computational reproducibility in high-dimensional classification tasks},
   journal = {Stat Appl Genet Mol Biol},
   volume = {3},
   pages = {Article37},
   year = {2004}
}


@Article{Sark2009,
   author = {Sarkar, D. and Parkin, R. and Wyman, S. and Bendoraite, A. and Sather, C. and Delrow, J. and Godwin, A. K. and Drescher, C. and Huber, W. and Gentleman, R. and Tewari, M.},
   title = {Quality assessment and data analysis for micro{RNA} expression arrays},
   journal = {Nucleic Acids Res},
   volume = {37},
   number = {2},
   pages = {e17},
   year = {2009}
}

@Article{Sarv2010,
   author = {Sarver, A. L.},
   title = {Toward understanding the informatics and statistical aspects of micro-{RNA} profiling},
   journal = {J Cardiovasc Transl Res},
   volume = {3},
   number = {3},
   pages = {204-11},
   year = 2010
}

@Article{Sato2009,
   author = {Sato, F. and Tsuchiya, S. and Terasawa, K. and Tsujimoto, G.},
   title = {Intra-platform repeatability and inter-platform comparability of micro{RNA} microarray technology},
   journal = {PLoS One},
   volume = {4},
   number = {5},
   pages = {e5540},
   year = {2009}
}

@Article{Smy2004,
   author = {Smyth, G. K.},
   title = {Linear models and empirical bayes methods for assessing differential expression in microarray experiments},
   journal = {Stat Appl Genet Mol Biol},
   volume = {3},
   pages = {Article3},
   year = {2004}
}

@INCOLLECTION{Smy2005a,
  AUTHOR =       {Smyth, G. K.},
  editor =       {Gentleman, R. and Carey, V. and Dudoit, S. and Irizarry, R. and Huber, W.},
  booktitle =    {Bioinformatics and Computational Biology Solutions using {R} and Bioconductor},
  title =        {\pkg{Limma}: linear models for microarray data},
  pages =        {397-420},
  PUBLISHER =    {Springer},
  YEAR =         {2005},
  address =      {New York}
}



@Article{Smy2005b,
   author = {Smyth, G. K. and Michaud, J. and Scott, H. S.},
   title = {Use of within-array replicate spots for assessing differential expression in microarray experiments},
   journal = {Bioinformatics},
   volume = {21},
   number = {9},
   pages = {2067-75},
   year = {2005}
}

@Article{Sub2005,
  author = {Subramanian, A. and Tamayo, P. and Mootha, V. K. and Mukherjee, S. and Ebert, B. L. and Gillette, M. A. and Paulovich, A. and Pomeroy, S. L. and Golub, T. R. and Lander, E. S. and Mesirov, J. P.},
   title = {Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles},
   journal = {Proc Natl Acad Sci U S A},
   volume = {102},
   number = {43},
   pages = {15545-50},
   year = {2005}
}


@Article{Tat2007,
   author = {Tatsuguchi, M. and Seok, H. Y. and Callis, T. E. and Thomson, J. M. and Chen, J. F. and Newman, M. and Rojas, M. and Hammond, S. M. and Wang, D. Z.},
   title = {Expression of micro{RNA}s is dynamically regulated during cardiomyocyte hypertrophy},
   journal = {J Mol Cell Cardiol},
   volume = {42},
   number = {6},
   pages = {1137-41},
   year = {2007}
}

@Article{Thom2007,
   author = {Thomson, J. M. and Parker, J. S. and Hammond, S. M.},
   title = {Microarray analysis of mi{RNA} gene expression},
   journal = {Methods Enzymol},
   volume = {427},
   pages = {107-22},
   year = {2007}
}

@Article{Troy2001,
   author = {Troyanskaya, O. and Cantor, M. and Sherlock, G. and Brown, P. and Hastie, T. and Tibshirani, R. and Botstein, D. and Altman, R. B.},
   title = {Missing value estimation methods for DNA microarrays},
   journal = {Bioinformatics},
   volume = {17},
   number = {6},
   pages = {520-5},
   year = {2001}
}


@Article{Tush2001,
   author = {Tusher, V. G. and Tibshirani, R. and Chu, G.},
   title = {Significance analysis of microarrays applied to the ionizing radiation response},
   journal = {Proc Natl Acad Sci U S A},
   volume = {98},
   number = {9},
   pages = {5116-21},
   year = {2001}
}


@Article{Wang2009,
   author = {Wang, V. and Wu, W.},
   title = {Micro{RNA}-based therapeutics for cancer},
   journal = {BioDrugs},
   volume = {23},
   number = {1},
   pages = {15-23},
   year = {2009}
}

@Article{Wang2007,
   author = {Wang, Y. and Stricker, H. M. and Gou, D. and Liu, L.},
   title = {Micro{RNA}: past and present},
   journal = {Front Biosci},
   volume = {12},
   pages = {2316-29},
   year = {2007}
}

@Article{Wang2010,
  author = {Wang, B. and Wang, X. F. and Howell, P. and Qian, X. and Huang, K. and Riker, A. I. and Ju, J. and Xi, Y.},
   title = {A personalized micro{RNA} microarray normalization method using a logistic regression model},
   journal = {Bioinformatics},
   volume = {26},
   number = {2},
   pages = {228-34},
   year = {2010}
}

@Article{Wet2004,
   author = {Wettenhall, J. M. and Smyth, G. K.},
   title = {limmaGUI: a graphical user interface for linear modeling of microarray data},
   journal = {Bioinformatics},
   volume = {20},
   number = {18},
   pages = {3705-6},
   year = {2004}
}

@Article{Zhan2007,
   author = {Zhan, M. and Miller, C. P. and Papayannopoulou, T. and Stamatoyannopoulos, G. and Song, C. Z.},
   title = {Micro{RNA} expression dynamics during murine and human erythroid differentiation},
   journal = {Exp Hematol},
   volume = {35},
   number = {7},
   pages = {1015-25},
   year = {2007}
}

@Article{Zhang2007,
   author = {Zhang, B. and Wang, Q. and Pan, X.},
   title = {Micro{RNA}s and their regulatory roles in animals and plants},
   journal = {J Cell Physiol},
   volume = {210},
   number = {2},
   pages = {279-89},
   year = {2007}
}

@Article{Zha2010,
   author = {Zhang, Z. and Florez, S. and Gutierrez-Hartmann, A. and Martin, J. F. and Amendt, B. A.},
   title = {MicroRNAs regulate pituitary development, and microRNA 26b specifically targets lymphoid enhancer factor 1 (Lef-1), which modulates pituitary transcription factor 1 (Pit-1) expression},
   journal = {J Biol Chem},
   volume = {285},
   number = {45},
   pages = {34718-28},
   year = 2010
}

%%%% OTHER REFERENCES %%%%%

%% R and Bioconductor URLs

@Manual{R2011,
       title        = {R: A Language and Environment for Statistical
                       Computing},
       author       = {{R Development Core Team}},
       organization = {R Foundation for Statistical Computing},
       address      = {Vienna, Austria},
       year         = 2011,
       url          = {http://www.R-project.org}
}
%%     note         = {{ISBN} 3-900051-07-0},

@webpage{bioc2011,
	title  = {Bioconductor - Home}, 
	url = {http://www.bioconductor.org/}
}

%% R / Bioconductor packages

@Manual{genefilter,
  title        = {\pkg{genefilter}: methods for filtering genes from microarray experiments}, 
  author       = {Gentleman, R. and Carey, V. and Huber, W. and Hahne, F.}, 
  year         = 2011,
  note         = {R package version 1.22-0},
  url          = {http://www.bioconductor.org/packages/2.3/bioc/html/genefilter.html}
}

@Manual{microRNA, 
  title        = {\pkg{micro{RNA}}: Data and functions for dealing with micro{RNA}s}, 
  author       = {Gentleman, R. and Falcon, S.}, 
  year         = 2011,
  note         = {R package version 1.10.0},
  url          = {http://www.bioconductor.org/packages/release/bioc/html/microRNA.html}
}


@Manual{RmiR.Hs.miRNA, 
  title        = {Various databases of micro{RNA} Targets}, 
  author       = {Favero, F.},
  year         = 2011,
  note         = {R package version 1.0.6},
  url          = {http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html}
}

@Manual{mirbase.db, 
  title        = {\pkg{miRBase}: the micro{RNA} database}, 
  author       = {Reid, J.F.}, 
  year         = 2011,
  note         = {R package version 0.6.0},
  url          = {http://www.bioconductor.org/packages/release/data/annotation/html/mirbase.db.html}
}


@Manual{targetscan.Hs.eg.db, 
  title        = {Target{S}can mi{RNA} target predictions for human}, 
  author       = {Reid, J.F.}, 
  year         = 2011,
  note         = {R package version 0.3.0},
  url          = {http://www.bioconductor.org/packages/release/data/annotation/html/targetscan.Hs.eg.db.html}
}

@Manual{targetscan.Mm.eg.db, 
  title        = {Target{S}can mi{RNA} target predictions for mouse}, 
  author       = {Reid, J.F.}, 
  year         = 2011,
  note         = {R package version 0.3.0},
  url          = {http://www.bioconductor.org/packages/release/data/annotation/html/targetscan.Mm.eg.db.html}
}


@Manual{GOstats,
  title        = {Tools for manipulating {GO} and microarrays}, 
  author       = {Gentleman, R. and Falcon, S.}, 
  year         = 2011,
  note         = {R package version 2.18.0},
  url          = {http://www.bioconductor.org/packages/release/bioc/html/GOstats.html}
}

%% URLs for miRNA target predictions

@webpage{pictar,
	title  = {Pic{T}ar},
	url = {http://pictar.mdc-berlin.de/}
}

@webpage{miRDB, 
	title  = {mi{RDB} - {M}icro{RNA} {T}arget {P}rediction and {F}unctional {S}tudy {D}atabase},
	url = {http://mirdb.org/miRDB/}
}

@webpage{miRanda,
	title  = {micro{RNA}.org}, 
	url = {http://www.microrna.org/microrna/home.do}	
}

@webpage{targetscan,
	title  = {{T}arget{S}can{H}uman 5.1},
	url = {http://www.targetscan.org/}
}

@webpage{microcosm,
	title  = {Micro{C}osm {T}argets},
	url = {http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/}
}


%% URLs for other databases

@webpage{geodata, 
	title  = {{GEO} DataSets home},
	url = {http://www.ncbi.nlm.nih.gov/gds/}
}


@webpage{kegg, 
	title  = {{KEGG PATHWAY} Database},
	url = {http://www.genome.jp/kegg/pathway.html}
}

@webpage{GO, 
	title  = {The {G}ene {O}ntology},
	url = {http://www.geneontology.org/}
}

%% URL for Miltenyi

@webpage{miltenyi, 
	title  = {{M}iltenyi {B}iotec: products \& services for biomedical research},
	url = {http://www.miltenyibiotec.com/en/default.aspx}
}


%% URL for Ingenuity Pathway Assist

@webpage{ingenuity, 
	title  = {{I}ngenuity {S}ystems, {R}edwood {C}ity, {CA}}, 
	url = {http://www.ingenuity.com}
}
