@string{AS =    {Annals of Statistics}}
@string{BI =    {Bioinformatics}}
@string{CancRes={Cancer Research}}
@string{ClinCh ={Clinical Chemistry}}
@string{PSB =   {Pacific Symposium on Biocomputing}}
@string{EMBOR = {EMBO Reports}}
@string{FEBSL=  {FEBS Letters}}
@string{GB =    {Genome Biology}}
@string{GR =    {Genome Research}}
@string{IJC =   {International Journal of Cancer}}
@string{JC =    {Journal of Classification}}
@string{JCB =   {Journal of Computational Biology}}
@string{JMVA =  {Journal of Multivariate Analysis}}
@string{JSPI =  {Journal of Statistical Planning and Inference}}
@string{JASA=   {Journal of the American Statistical Association}}
@string{JCGS=   {Journal of Computational and Graphical Statistics}}
@string{JRSSB=	{Journal of the Royal Statistical Society, Series B}}
@string{MBC =   {Molecular Biology of the Cell}}
@string{MC =    {Molecular Cell}}
@string{ML =    {Machine Learning}}
@string{NAR =   {Nucleic Acids Res}}
@string{NCB =   {Nature Cell Biology}}
@string{NBT =   {Nature Biotechnology}}
@string{NG  =   {Nature Genetics}}
@string{PRL =   {Physical Review Letters}}
@string{PSB =   {Pacific Symposium on Biocomputing}}
@string{PNAS =  {Proc. Natl. Acad. Sci. of the U.S.A.}}
@string{SAGMB = {Statistical Applications in Genetics and Molecular Biology}}
@string{SM =    {Statistics in Medicine}}
@string{SN =    {Social Networks}}

@book{Silverman,
  author = {B. W. Silverman}, 
  year  = {1986}, 
  title = {Density Estimation for Statistics and Data Analysis}, 
  publisher  = {Chapman and Hall},
  location =  {London},
}

@article{KEGG,
  author =       {Kanehisa, M. and Goto, S.},
  title =        {KEGG: Kyoto Encyclopedia of Genes and Genomes},
  journal =      {Nucleic Acids Research},
  volume =       {28},
  year =         {2000},
  pages =        {27--30},
}

@Article{GO,
  author =       {{The Gene Ontology Consortium}},   
  title =        {{G}ene {O}ntology: tool for the unification of biology},
  journal =      {Nature Genetics},
  year =         {2000},
  volume =       {25},
  pages =        {25-29},
}




@article{SGD,
 author = {R. Balakrishnan and K. R. Christie and M. C. Costanzo and others},
 title = {Saccharomyces Genome Database},
 url = {http://www.yeastgenome.org/},
 year = {2006}
}

@article{Deutschbauer2005a,
 title = {Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling 
   in Yeast},
 author = {A. M. Deutschbauer and D. F. Jaramillo and M. Proctor and others},
 journal = {Genetics},
 volume = {169},
 pages = {1915--1925},
 year = {2005},
}






@ARTICLE{Balasubramanian2004,
  author = {R. Balasubramanian and T. LaFramboise and D. Scholtens
	and R. Gentleman},
  title = {{A} graph-theoretic approach to testing associations between disparate
	sources of functional genomics data.},
  journal = {Bioinformatics},
  year = {2004},
  volume = {20},
  pages = {3353--3362},
  number = {18},
  month = {Dec},
  abstract = {MOTIVATION: The last few years have seen the advent of high-throughput
	technologies to analyze various properties of the transcriptome
	and proteome of several organisms. The congruency of these different
	data sources, or lack thereof, can shed light on the mechanisms
	that govern cellular function. A central challenge for bioinformatics
	research is to develop a unified framework for combining the multiple
	sources of functional genomics information and testing associations
	between them, thus obtaining a robust and integrated view of the
	underlying biology. RESULTS: We present a graph-theoretic approach
	to test the significance of the association between multiple disparate
	sources of functional genomics data by proposing two statistical
	tests, namely edge permutation and node label permutation tests.
	We demonstrate the use of the proposed tests by finding significant
	association between a Gene Ontology-derived predictome and data
	obtained from mRNA expression and phenotypic experiments for Saccharomyces
	cerevisiae. Moreover, we employ the graph-theoretic framework to
	recast a surprising discrepancy presented elsewhere between gene
	expression and knockout phenotype, using expression data from a
	different set of experiments. AVAILABILITY: An R software package,
	GraphAT, containing the data and statistical procedures is available
	from Bioconductor: http://www.bioconductor.org.},
  doi = {10.1093/bioinformatics/bth405},
  keywords = {Algorithms, Biological, Cell Physiology, Chromosome Mapping, Comparative
	Study, Computer Simulation, Computer-Assisted, DNA, Gene Expression
	Profiling, Gene Expression Regulation, Models, Numerical Analysis,
	P.H.S., Protein Interaction Mapping, Proteome, Re, Reproducibility
	of Results, Saccharomyces cerevisiae, Sensitivity and Specificity,
	Sequence Alignment, Sequence Analysis, Signal Transduction, Transcription
	Factors, U.S. Gov't, search Support, 15256415},
  owner = {Nolwenn},
  pii = {bth405},
  pmid = {15256415},
  timestamp = {2006.02.24},
  url = {http://dx.doi.org/10.1093/bioinformatics/bth405},
}





@ARTICLE{Chiang2007,
  author = {T. Chiang and D. Scholtens and D. Sarkar and R. Gentleman and W. Huber},
  title = {{C}overage and error models of protein-protein interaction data by directed graph
analysis.},
  journal = {Genome Biology},
  year = {2007},
  volume = {8},
  pages = {R186},
  number = {9},
  month = {sep},
  pmid = {17845715},
}


@ARTICLE{Davierwala2005,
  author = {P.A. Davierwala and J. Haynes and Z. Li and R.L. Brost and
                  M.D. Robinson and L. Yu and S. Mnaimneh and H. Ding
                  and H. Zhu and Y. Chen and X. Cheng and G.W.
                  Brown and C. Boone and B.J. Andrews and
                  T.R. Hughes},
  title = {{T}he synthetic genetic interaction spectrum of essential genes.},
  journal = {Nat Genet},
  year = {2005},
  volume = {37},
  pages = {1147--1152},
  number = {10},
  month = {Oct},
  abstract = {The nature of synthetic genetic interactions involving essential genes
	(those required for viability) has not been previously examined
	in a broad and unbiased manner. We crossed yeast strains carrying
	promoter-replacement alleles for more than half of all essential
	yeast genes to a panel of 30 different mutants with defects in diverse
	cellular processes. The resulting genetic network is biased toward
	interactions between functionally related genes, enabling identification
	of a previously uncharacterized essential gene (PGA1) required for
	specific functions of the endoplasmic reticulum. But there are also
	many interactions between genes with dissimilar functions, suggesting
	that individual essential genes are required for buffering many
	cellular processes. The most notable feature of the essential synthetic
	genetic network is that it has an interaction density five times
	that of nonessential synthetic genetic networks, indicating that
	most yeast genetic interactions involve at least one essential gene.},
  doi = {10.1038/ng1640},
  keywords = {Essential, Fungal, Gene, Gene Expression Regulation, Genes, Non-U.S.
	Gov't, Research Support, Saccharomyces cerevisiae, Saccharomyces
	cerevisiae Proteins, s, 16155567},
  owner = {Nolwenn},
  pii = {ng1640},
  pmid = {16155567},
  timestamp = {2006.02.24},
  url = {http://dx.doi.org/10.1038/ng1640},
}


@article{Dudley2005,
 title = {A global view of pleiotropy and phenotypically derived gene function in yeast},
 author = {A. M. Dudley and D. M. Janse and A. Tanay and R. Shamir and G. McDonald Church},
 journal = {Molecular Systems Biology},
 volume = {1},
 pages = {E1--E11},
 year = {2005},
}






@ARTICLE{Giaever2002,
 author= {G. Giaever and others},
  title = {Functional profiling of the Saccharomyces cerevisiae genome.},
  journal = {Nature},
  year = {2002},
  volume = {418},
  pages = {387--391},
  number = {6896},
  month={Jul},
  owner = {Nolwenn},
  pii = {nature00935},
  pmid = {12140549},
  timestamp = {2006.03.10},
  url = {http://dx.doi.org/10.1038/nature00935},
}  




@ARTICLE{Kastenmayer2005,
author = {J.P. Kastenmayer and L. Ni and A. Chu and L.E. Kitchen and
                  W.C. Au and H. Yang and C.D. Carter and D. Wheeler and
                  R.W. Davis and J.D. Boeke and M.A. Snyder and M.A. Basrai},
title ={Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.},
journal = {Genome Research},
year = {2006}, 
volume = {16},
number = {3},
pages = {365--373},
pmid = {16510898},
} 




@ARTICLE{Lesage2005,
author = {G. Lesage and J. Shapiro and C.A. Specht and A.M. Sdicu and
                  P. Menard and S. Hussein and A.H. Tong and C. Boone
                  and H. Bussey},
title = {{A}n interactional network of genes involved in chitin synthesis in Saccharomyces
cerevisiae.},
journal = {BMC Genet.},
year={2005},
volume = {6},
number = {1},
pages = {1--8},
 pmid = {15715908},
}



@ARTICLE{Osterberg2006,
author = {M. Osterberg and H. Kim and J. Warringer and K. Melen and A. Blomberg and G. von Heijne},
title = {{P}henotypic effects of membrane protein overexpression in Saccharomyces cerevisiae.},
journal = {PNAS},
year={2006},
volume = {103},
number = {30},
pages = {11148--53}, 
pmid = {16847257},
}

@Article{Spirin2006,
  author =       {V. Spirin and M.S. Gelfand and  A.A. Mironov and L.A. Mirny}, 
  title =        {A metabolic network in the evolutionary context: multiscale structure and modularity.},
  journal =      {PNAS},
  year =         {2006},
  volume =       {23},
  pages =        {8774--8779}
}