@article{jaccard:1912,
  author={Jaccard, P.},
  title={The distribution of flora in the alpine zone},
  year={1912},
  journal={The New Phytologist},
  volume={11},
  issue={2},
  pages={37-50}
}

@InCollection{WileyEncy,
 title = {Differential Expression with the Bioconductor Project},
 author = {A. von Heydebreck and W. Huber and R. Gentleman},
 year = {2004},
 booktitle= {Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics},
 publisher = {John Wiley and Sons},
}

@Article{GOA,
   author = {E. Camon and M. Magrane and D. Barrell and V. Lee and
                  E. Dimmer and J. Maslen, 
          D. Binns and N. Harte and R. Lopez and R. Apweiler},
   year = {2004},
   title = {The {G}ene {O}ntology Annotation ({GOA}) Database: sharing
         knowledge in {U}niprot with {G}ene {O}ntology},  
   journal = {Nucleic Acids Research},
   volume = {32},
   issue = {1},
   pages = {D262--D266}
 }
 
@Article{GentTL,
author = {R. Gentleman and D. {Temple Lang}},
title = {Statistical Analyses and Reproducible Research},
publisher = {Submitted},
year = {2003}
} 

@Article{GentGO2004B,
author = {R. Gentleman},
title = {Hypothesis Testing and {GO}},
publisher = {Manuscript},
year = {2003}
} 

@ARTICLE{Lordetal,
  AUTHOR = {P.W.Lord and R.D. Stevens and A. Brass and
                  C.A.Goble},
  TITLE = {Investigating semantic similarity measures across
                  the {Gene Ontology}: the relationship between
                  sequence and annotation.},
  JOURNAL = {Bioinformatics},
  YEAR = 2003,
  PAGES = {1275-83},
  VOLUME = 19,
  NUMBER = 10,
}
@book{hubert:1987,
  author={Hubert, L. H.},
  year={1987},
  title={Assignment Methods in Combinatorial Data Analysis},
  publisher={Dekker},
  location={ New York}
}



@techreport{ GXL,
    author = "Andreas Winter",
    title = "{Exchanging Graphs with {GXL}}",
    number = "9--2001",
    address = "Universit{\"a}t Koblenz-Landau, Institut f{\"u}r
    Informatik, Rheinau 1, D-56075 Koblenz",  
    year = "{2001}",
    url = "citeseer.nj.nec.com/article/winter01exchanging.html" }

@techreport{Raji,
  author = {R. Balasubraminian and T. La{F}ramboise and D. Scholtens and 
     R. Gentleman},
  title = {Integrating disparate sources of protein--protein
  interaction data},  
  institution = {Bioconductor},
  year = {2004},
}

@techreport{Scholtens,
  author = {D. Scholtens and R. Gentleman},
  title = {Predicting Protein Complex Membership using Affinity Purification
   Data},
  institution = {Bioconductor},
  year = {2004},
}

@techreport{WattsRG,
  author = {M. E. J. Newman and S. H. Strogatz and D. J. Watts},
  title = {Random graphs with arbitrary degree distributions and their
  applications}, 
  year = {2001},
  institution = {Cornell University},
}

@techreport{NewmanRG,
  author = {M. E. J. Newman},
  title = {Random graphs as models of networks},
  year = {2002},
  institution = {Santa {F}e {I}nstitute},
}

@Article{ErdosRenyi,
  author = {P. Erd\"{o}s and A. R\'{e}nyi},
  title  = {On random graphs},
  journal = {Publicationes Mathematicae},
  volume = {6},
  pages = {290--297},
  year = {1959}
}

@book{Sedgewick,
  author = {Robert Sedgewick},
  title = {Algorithms, 3rd {E}dition},
  publisher ={Addison Wesley},
  year = {2002}
}

@book{IntroAlgs,
 author = {T. H Cormen and C. E. Leiserson and R. L. Rivest and
 C. Stein},
 title = {Introduction to Algorithms, 2nd {E}dition},
 publisher = {The M{I}{T} {P}ress},
 year = {2001}
}

@book{Siek,
 author="Jeremy G. Siek and Lie-Quan Lee and Andrew Lumsdaine",
 title="The Boost Graph Library",
 publisher="Addison Wesley",
 year = 2002,
 pages = 322}

@Article{HovigNG,
  author = {T.-{K}. Jenssen and A. Laegreid and J. Komorowski and
  E. Hovig},
  title = {A literature network of human genes for high-throughput
  analysis of gene expression},
  journal = {Nature Genetics},
  year = {2001},
  pages = {21--28}
}

@Article{Gavin,
  author = 	 {Gavin, A.-C. and others},
  title = 	 {Functional organization of the yeast proteome by
                  systematic analysis of protein complexes}, 
  journal = 	 {Nature},
  year = 	 {2002},
  volume = 	 {415},
  pages = 	 {141-147}
}

@Article{Ito,
  author = 	 {Ito, T. and others},
  title = 	 {A comprehensive two-hybrid analysis to explore the
                  yeast protein interactome}, 
  journal = 	 {Proc. Nat. Acad. Sci. U.S.A.},
  year = 	 {2001},
  volume = 	 {98},
  pages = 	 {4569-4574}
}


@Article{Lee2002, 
  author = {T. I. Lee and N. J. Rinaldi and F. Robert
  and D. T. Odom and Z. Bar-{J}oseph and G. K. Gerber and N. M Hannett
  and C. T. Harbison and C. M Thompson and I. Simon and J. Zeitlinger
  and E. G. Jennings and H. L. Murray and D. B. Gordon and B. Ren and
  J. J. Wyrick and J-{B}. Tagne and T. L. Volkert adn E. Fraenkel and
  D. K. Gifford and R. A. Young},
  title = {Transcriptional Regulatory Networks in
  \textit{Saccharomyces cerevisiae}},
  journal = {Science},
  year = {2002},
  volume = {298},
  pages = {799--804}
}

@Article{Alon2002,
  author = {R. Milo and S. Shen-{O}rr and S. Itzkovitz and N. Kashtan
  and D. Chklovskii and U. Alon},
  title = {Network Motifs: Simple building blocks of complex networks},
  journal = {Science},
  year = {2002},
  volume = {298},
  pages = {824--827},
}

@Article{Bork2003,
  author = {R. Krause and C. von {M}ering and P. Bork},
  title = {A comprehensive set of protein complexes in yeast: mining
  large scale protein-protein interaction screens},
  journal = {Bioinformatics},
  year = {2003},
  volume = {19},
  pages = {1901-1908},
}

@Article{Gerstein-JSFG,
  author = {R. Jansen and N. Lan and J. Qian and M. Gerstein},
  title = {Integration of genomic datasets to predict protein
  complexes in yeast},
  journal = {Journal of Structural and Functional Genomics},
  year = {2002},
  pages = {1--11},
  volume = {00}
}

@Article{Gerstein-GR,
  author = {R. Jansen and D. Greenbaum and M. Gerstein},
  title = {Relating whole-genome expression data with protein-protein
  interactions},
  journal = {Genome Research},
  year = {2002},
  pages = {37--45}
}

@Article{LockhartN,
   author = {R. J. Cho and M. Huang and M. J. Campbell and H. Dong and
   L. Steinmetz and L. Sapinoso and G. Hampton and S. J. Elledge and
   D. J. Lockhart},
   title = {Transcriptional regulation and function during hte human
   cell cycle},
   journal = {Nature Genetics},
   year = {2001},
   pages = {48--54},
   volume = {27}
}

@Article{Strogatz,
   author = {S. H. Strogatz},
   title = {Exploring complex networks},
   journal = {Nature},
   year = {2001},
   pages = {268--276},
   volume = {410},
}

@Article{FriedmanNG,
  author = {E. Segal and M. Shapira and A. Regev and D Pe'er and
  D. Botstein and D. Koller},
  title = {Module networks: identifying regulatory modules and their
  condition-specific regulators from gene expression data},
  journal = {Nature Genetics},
  year = {2003},
  pages = {166--176},
  volume = {34}
}

@InProceedings{McCrayetal,
  author = 	 {A. T. McCray and A. C. Browne and O. Bodenreider},
  title = 	 {The Lexical Properties of the {G}ene {O}ntology ({GO})},
  booktitle = 	 {Proceedings of the AMIA 2002 Annual Symposium},
  pages =	 {504--508},
  year =	 {2002},
}

%%%%RI: BIBLIOGRAPHY FOR RELATED PROJECTS 

@Manual{affy, 
 title = {Affymetrix Microarray Suite User Guide}, 
 author  = {Affymetrix}, 
 year = {2001}, 
 organization = {Affymetrix}, 
 address  = {Santa Clara, CA}, 
 edition = {version 5}, 
}

@Manual{rosetta,
   title = 	 {Rosetta Resolver system},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {Rosetta Biosoftware},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.rosettabio.com/products/resolver/default.htm},
   annote =	 {http://www.rosettabio.com/products/resolver/default.htm}
 }

@Manual{xml,
   title = 	 {XML for Molecular Biology},
   author =	 {Paul Gordon},
   OPTorganization = {},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   OPTnote = 	 {http://maggie.cbr.nrc.ca/~gordonp/xml/},
   OPTannote = 	 {http://maggie.cbr.nrc.ca/~gordonp/xml/}
 }

@Manual{biodas,
   title = 	 {Biodas},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {Biodas},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://biodas.org/},
   annote =	 {http://biodas.org/}
 }

@Manual{bioperl,
   title = 	 {bioperl},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {bioperl},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.bioperl.org/},
   annote =	 {http://www.bioperl.org/}
 }

@Manual{genomax,
   title = 	 {GenoMax},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {Informax},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.informaxinc.com/solutions/genomax/index.html},
   annote =	 {http://www.informaxinc.com/solutions/genomax/index.html}
 }

@Manual{spotfire,
   title = 	 {Spotfire
   DecisionSite for Functional Genomics},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {Spotfire},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.spotfire.com/products/fg.asp},
   annote =	 {http://www.spotfire.com/products/fg.asp}
 }

@Article{sam,
	     author =   {Tusher, V. and  Tibshirani, R. and Chu, C},
	     title =    {Significance analysis of microarrays applied to
			 ionizing radiation response},
	     volume = {98},
	     year = {2001},
	     journal = {Proceedings of the National Academy of Sciences USA},
	     pages = {5116--5121},
   annote =	 {http://www-stat.stanford.edu/~tibs/SAM/index.html}
 }

@Manual{genespring,
   title = 	 {GeneSpring},
   author =	 {Andrew R. Conway},
   organization = {Silicon Genetics},
   address =	 {Redwood City, CA},
   edition =	 {4.2},
   year =	 {2001},
   note =	 {http://www.sigenetics.com/cgi/SiG.cgi/index.smf},
   annote =	 {http://www.sigenetics.com/cgi/SiG.cgi/index.smf}
 }

@Article{Chiaretti2004,
 author = { S. Chiaretti and X Li and R Gentleman and A Vitale and 
M. Vignetti and F. Mandelli and J.  Ritz and and R. Foa},
  year = {2004},
 title = {Gene expression profile of adult T-cell acute lymphocytic leukemia
identifies distinct subsets of patients with different response to therapy
and survival},
  journal = {Blood},
  pages = {2771--2778},
  volume = {103}
}

@Article{Irizarry2003,
 author = {R. A. Irizarry and B. Hobbs and F. Collin and Y. D. Beazer-Barclay
 and K. J.  Antonellis and U. Scherf and T. P. Speed},
 title={ Exploration, normalization, and summaries of high density
  oligonucleotide array probe level data},
 journal = {Biostatistics},
 year = {2003},
 volume = {4},
 pages = {249--264},
}

@Article{Huber2002,
 author = {W. Huber and A. von Heydebreck and H.  {S\"ultmann} and A. Poustka
 and M. Vingron},
 title = {Variance Stabilization Applied to Microarray Data Calibration and 
  to the Quantification of Differential Expression},
 journal = {Bioinformatics}, 
 volume = {18 Suppl. 1},
 pages = { S96--S104},
 year = {2002},
}

@Article{gmep,
   author = 	 {D. Y. Chiang and P. O. Brown and M. Eisen},
   title = 	 {Visualizing associations between genome sequence and
   gene expression data using genome-mean expression profiles}, 
   journal = 	 {Bioinformatics},
   year = 	 {2001},
   volume =	 {17},
   pages =	 {S49--S55},
   annote =	 {http://rana.lbl.gov/EisenSoftware.htm}
 }

@Article{LOH2000,
  author = {K. Lindblad--Toh and D. M. Tanenbaum and M. J. Daly and
  E. Winchester and W. O. Liu and A. Villpakkam and S. E. Santon and
  C. Larrson and T. J. Hudson and B. E. Johnson and E. S. Langer and
  M. Meyerson},
   title = {Loss--of--heterozygosity analysis of small--cell lung
  carcinomas using single--nucleotide polymorphism arrays},
   journal = {Nature Biotechnology},
   year = {2000},
   volume = {18},
   pages = {1001--1005},
}

@Article{Meyerson2002,
  author = {G. Weber and J. Shendure and D. M. Tannenbaum and G. M. Church
  and M. Meyerson},
   title = {Identification of foreign gene sequences by transcript
  filtering against the human genome},
   journal = {Nature Genetics},
   year = {2002},
   volume = {30},
   pages = {141--2},
}


@Manual{genesight,
   title = 	 {GeneSight},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {BioDiscovery, Inc.},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.biodiscovery.com/genesight.asp},
   annote =	 {http://www.biodiscovery.com/genesight.asp}
 }

@Article{cluster,
   author = 	 {M. B. Eisen and P. T. Spellman and P.
   O. Brownand and D. Botstein}, 
   title = 	 {Cluster analysis and display of genome-wide
   expression patterns}, 
   journal = 	 {Proceedings of the National Academy of Sciences USA},
   year = 	 {1998},
   volume =	 {95},
   number =	 {25},
   pages =	 {14863--14868},
   annote =	 {http://rana.lbl.gov/EisenSoftware.htm}
 }

@Article{Mutter2000,
   author = 	 {G. L. Mutter and J. P. A. Baak and J.
   T. Fitzgerald and R. Gray and D. Neuberg and G. A. Kust
   and R. Gentleman and S. R. Gullans and L.-J. Wei and M. Wilcox},
   title = 	 {Global Expression Changes in Constitutive and Hormonally Regulated Genes during Endometrial Neoplastic Transformation},
   journal = 	 {Gynecologic Oncology},
   year = 	 {2001},
   volume =	 {83},
   number =	 {},
   pages =	 {177-185},
   annote =	 {www.idealibrary.com}
 }

@Manual{cybert,
   title = 	 {CyberT},
   OPTkey = 	 {},
   author =	 {Tony Long and Harry Mangalam},
   organization = {National Center for Genome Resources},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://genomics.biochem.uci.edu/genex/cybert/},
   annote =	 {http://genomics.biochem.uci.edu/genex/cybert/}
 }

 %cDNA Microarray analysis.
@Article{cdnama, 
   author = 	 {G. C. Tseng and M.-K. Oh and L. Rohlin and J. C. Liao and W. H. Wong},
   title = 	 { Issues in cDNA microarray
 analysis: {Q}uality filtering, channel normalization, models of variations and assessment of gene effects,},
   journal = 	 {Nucleic Acids
 Res},
   year = 	 {2001},
   volume =	 {29},
   pages =	 {2549},
   annote =	 {http://biosun1.harvard.edu/~ctseng/download.html}
 }

@Article{dchip,
   author = 	 {Cheng Li and Wing Hung Wong},
   title = 	 { Model-based analysis of oligonucleotide arrays:
 Expression index computation and outlier detection},
   journal = 	 {Proceedings of the National Academy of Sciences USA},
   year = 	 {2001},
   volume =	 {98},
   pages =	 {31--36},
   annote =	 {http://biosun1.harvard.edu/~cli/dchip\_request.htm},
 }

@Manual{genex,
   title = 	 {GeneX},
   OPTkey = 	 {},
   OPTauthor = 	 {},
   organization = {National Center for Genome Resources and Computational Genomics Group at the University of California, Irvine},
   OPTaddress = 	 {},
   OPTedition = 	 {},
   OPTmonth = 	 {},
   OPTyear = 	 {},
   note =	 {http://www.ncgr.org/genex/},
   OPTannote = 	 {}
 }

@Article{Carey1997,
  author = {V. J. Carey},
  title = {Using hypertext and the internet for structure and
  management of observational studies},
  journal = {Statistics in Medicine},
   year = {1997},
   volume = {16},
   pages = {1667-1682},
}

@Article{genecluster,
   author = 	 {P. Tamayo and D. Slonim and J. Mesirov and Q. Zhu and S. Kitareewan and E. Dmitrovsky and E. S. Lander and and T. R. Golub},
   title = 	 {Interpreting patterns of gene expression with self-organizing maps},
   journal = 	 {Proceedings of the National Academy of Science USA},
   year = 	 {1999},
   volume =	 {96},
   pages =	 {2907--2912},
   annote =	 {http://www-genome.wi.mit.edu/cancer/software/software.html},
 }

 @InProceedings{iriz:etal:2001,
  author = 	 {R. A. Irizarry and G. Parmigiani and M. Guo and T. Dracheva and  J. Jen},
  title = 	 {A Statistical Analysis of Radiolabeled Gene Expression Data},
  booktitle = 	 {Proceedings of Interface 2001},
  pages =	 {1--4},
  year =	 {2001},
  address =	 {Orange County, CA},
}
 %%%%RI: Bibliography for Application by RI



@Article{iriz:etal:2002,
  author = {R. A. Irizarry and B. Hobbs and F. Collin and Y. D. Beazer-Barclay and K. J. Antonellis and U. Scherf and T. P. Speed},
  title = 	 {Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data},
journal = {Submitted},
  note = 	 {http://biosun01.biostat.jhsph.edu/~ririzarr/papers},
  year = 	 {2002},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{hill:etal:2000,
  author = 	 {A.A. Hill and C.P Hunter and B.T. Tsung and G. Tucker-Kellogg and E.L. Brown},
  title = 	 {Genomic Analysis of Gene Expression in C. elegans},
  journal = 	 {Science},
  year = 	 {2000},
  OPTkey = 	 {},
  volume =	 {290},
  OPTnumber = 	 {},
  pages =	 {809--812},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@Article{hill:etal:2001,
  author = 	 {Andre A. Hill and Eugene L. Brown and Maryann Z. Whitley and Greg Tucker-Kellogg and Craig P. Hunter and Donna K. Slonim},
  title = 	 {Evaluation of normalization procedures for oligonucleotide array data based on spiked c{RNA} controls},
  journal = 	 {Genomebiology},
  year = 	 {2001},
  OPTkey = 	 {},
  volume =	 {2},
  pages =	 {1--13},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{baug:etal:2001,
  author = 	 {L.R. Baugh and A.A. Hill and E.L. Brown and Craig P. Hunter},
  title = 	 {Quantitative analysis of m{RNA} amplification by {\it in vitro} transcription},
  journal = 	 {Nucleic Acids Research},
  year = 	 {2001},
  volume =	 {29},
  OPTnumber = 	 {},
  pages =	 {1--9},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@TechReport{affy:tech:2001,
  author = 	 {Affymetrix},
  title = 	 {New Statistical Algorithms for Monitoring Gene
  Expression on $\mbox{GeneChip}^{\mbox{\textregistered}}$ Probe
  Arrays}, 
  institution =  {Affymetrix},
  year = 	 {2001},
}

@InProceedings{affytalk:2001,
   title = 	 {Estimating Signal with Next Generation {A}ffymetrix Software},
  author = 	 {Earl Hubbell},
booktitle = 	 {Gene Logic Workshop on Low Level Analysis of Affymetrix $\mbox{GeneChip}^{\mbox{\textregistered}}$ data},
  year =	 {2001},
  note =	 {{\small \tt http://www.stat.berkeley.edu/users/terry/zarray/Affy/GL\_Workshop/genelogic2001.html}}
}

@InProceedings{fang:li:wong:2001,
   title = 	 {Model-based Saturation Handling},
  author = 	 {Xuemin Fang and Cheng Li and Wing Hung Wong},
booktitle = 	 {Genelogic Workshop on Low Level Analysis of Affymetrix $\mbox{GeneChip}^{\mbox{\textregistered}}$ data},
  year =	 {2001},
  note =	 {{\small \tt http://www.stat.berkeley.edu/users/terry/zarray/Affy/GL\_Workshop/genelogic2001.html}}
}


@InProceedings{hold:etal:2001,
  author = 	 {Daniel Holder and Richard F. Raubertas and V. Bill Pikounis and Vladimir Svetnik and Keith Soper},
  title = 	 {Statistical analysis of high density oligonucleotide arrays: {A} {SAFER} approach},
    year = 	 {2001},
  booktitle = 	 {Proceedings of the ASA Annual Meeting, Atlanta, GA 2001},
  OPTcrossref =  {},
  OPTkey = 	 {},
  OPTpages = 	 {},
  OPTyear = 	 {},
  OPTeditor = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTorganization = {},
  OPTpublisher = {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{astr:2001,
  author = 	 {Magnus {\AA}strand},
  title = 	 {Normalizing oligonucleotide arrays},
  journal = 	 {Unpublished manuscript},
  year = 	 {2001},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{bols:2001,
  author = 	 {Ben Bolstad},
  title = 	 {Probe level quantile normalization of high density oligonucleotide arrays},
  journal = 	 {Unpublished manuscript},
  year = 	 {2001},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{dudo:etal:2001,
  author =       {S. Dudoit and Y. H. Yang and M. J. Callow and T. P. Speed},
  title =        {Statistical methods for identifying genes with differential
expression in replicated  c{DNA} microarray experiments},
  journal =      {Statistica Sinica},
  year =         {2001},
  OPTkey =       {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTpages =     {},
  OPTmonth =     {},
  note =	 {Accepted},
  OPTannote =    {}
}

@Article{li:wong:2001a,
   Author = {Li, C. and Wong, W.H.},
   Title = {Model-based analysis of oligonucleotide arrays: {E}xpression index computation and outlier detection},
   Journal = {Proceedings of the  National Academy of Science USA},
   Year = 2001,
   Volume = {98},
   Pages = {31--36},
} 

@Article{li:wong:2001b,
   Author = {Li, C. and Wong, W.H.},
   Title = {Model-based analysis of oligonucleotide arrays: {M}odel validation, design issues and standard error application},
   Journal = {Genome Biology},
   Year = 2001,
   Volume = {2},
   Pages = {1--11}
} 

@Article{lock:etal:1996,
   Author = {David J. Lockhart and Helin Dong and Michael C. Byrne and Maximillian T. Follettie and Michael V. Gallo and Mark S. Chee and Michael Mittmann and Chunwei Wang and Michiko Kobayashi and Heidi Horton and Eugene L. Brown},
   Title = {Expression Monitoring by hybridization to high-density oligonucleotide arrays},
   Journal = {Nature Biotechnology},
   Year = 1996,
   Volume = {14},
   Pages = {1675--1680}
}


@InProceedings{hart:etal:2001,
  author = 	 {Alexander J. Hartemink and David K. Gifford and Tommi S. Jaakola and Richard A. Young},
  title = 	 {Maximum likelihood estimation of optimal scaling factors for expression array normalization},
  booktitle = 	 {SPIE BiOS},
  year =	 2001,
  month =	 {January},
  annote =	 {affymetrix, high density oligonucleotide}
}




@Article{efro:etal:2001,
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@Article{naef:etal:2001,
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   Pages = {1--9}
} 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SD biblio

@string{JASA= {Journal of the American Statistical Association}}
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@Unpublished{Dudoit&Shaffer02,
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SD added 17/11/2002

@Article{Brazmaetal01,
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@Misc{apcomplex,
  note = 	 {\texttt{apComplex} is available at http://www.bioconductor.org.}
}

@Misc{rawTAP,
  note = 	 {The 589 purifications are available in Supplementary Table 1 of Gavin et al. at http://www.nature.com.   }
}

@Misc{yTAP,
  note = 	 {The 232 annotated ``yTAP'' complexes are available in Supplementary Table 3 of Gavin et al. at http://www.nature.com and at http://yeast.cellzome.com.}
}

@Misc{ourTAP,
  note = 	 {Our 720 estimated TAP complexes are available at http://www.bioconductor.org/Docs/Papers/2003/apComplex.}
}

@Misc{HMSPCI,
  note = 	 {The HMS-PCI raw purification data is available at http://www.mdsp.com/yeast.}
}

@Misc{ourHMSPCI,
  note = 	 {Our 1008 HMS-PCI estimated complexes are available at http://www.bioconductor.org/Docs/Papers/2003/apComplex.}
}

@Misc{MIPS,
  note = 	 {We used the 267 MIPS complexes reported at ftp://ftpmips.gsf.de/ yeast/catalogues/complexes/complex$\_$130603.}
}

@Misc{cellcycle,
  note = 	 {The 30 expression clusters are available at  http://arep.med.harvard.edu/ network$\_$discovery/.}
}

@Misc{sensspec,
  note = 	 {Perfect sensitivity (specificity) means zero probability of FN (FP) observations.}
}

@Misc{CCGcols,
  note = 	 {Proteins that are used as baits are yellow, and proteins that are only found as hits are white.  Complex comemberships for pairs of proteins that are both baits are tested twice, once during each respective purification.  In the CCG, red reciprocated bait-bait edges represent existing doubly tested complex comemberships.  For bait-hit-only pairs, complex comembership is only tested once since the hit-only protein is never used as a bait.  In the CCG, gray unreciprocated edges from baits to non-baits represent existing singly tested complex comemberships.}
}

@Misc{omega,
  note = 	 {For two complexes $C_A$ and $C_B$ of size $a$ and $b$, respectively, with $i$ proteins in common, $\omega$ measures the percentage of proteins in common from the point of view of both complexes, and chooses the minimum as a conservative measure of overlap.  }
}


@Misc{nodeperm,
  note = 	 {Conditioning on the structure of the TAP graph, we randomly reassigned the node labels and counted the number of intracluster edges for each permutation.}
}


@Misc{ack,
  note = 	 {We thank M. Vidal for critical discussions.  The authors were supported by grant P20 CA96470.}
}





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