%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% This file should contain the bib references for a chapter of the
%% volume "Bacterial Molecular Networks" of the series "Methods in
%% Molecular Biology".


%% Some examples used in the template chapter.
%%
%% More detailed formatting examples can be found in the accompanying 
%% file bibtex_templates.tex

@article{Gabor2006,
    title = {The igraph software package for complex network research},
    author = {Gabor Csardi and Tamas Nepusz},
    journal = {InterJournal},
    volume = {Complex Systems},
    pages = {1695},
    year = {2006}
  }

@article{Scholtens2005,
  author = {D. Scholtens and M. Vidal and R. Gentleman},
  title = {Local dynamic modeling of global interactome networks},
  journal = {Bioinformatics},
  year = {2005},
  volume = {21},
  pages = {3548--3557}
}

@article{VSN,
    title = {Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression},
    author = {Wolfgang Huber and Anja von Heydebreck and Holger Sueltmann and Annemarie Poustka and Martin Vingron},
    journal = {Bioinformatics},
    year = {2002},
    volume = {18 Suppl. 1},
    pages = {S96-S104},
  }

@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},
 }

@article{biomart,
 journal = {Nucleic Acids Res.},
 year = {2009},
 pages = {W23-7},
 title = {BioMart Central Portal--unified access to biological data},
 author = {Haider, S. and Ballester, B. and Smedley, D. and Zhang, J. and Rice, P. and  Kasprzyk, A.},
}

@book{SNA,
  author =       {Wasserman, Stanley and Faust, Katherine},
  title =        {Social Network Analysis, Methods and Applications},
  publisher =    {Cambridge University Press},
        address = {Cambridge},
  year =         {1994}
}

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


@book{MASS,
  author =       {W. N. Venables and B. D. Ripley},
  year =         {2002},
  title =        {Modern Applied Statistics with S (4e)},
  publisher =    {Springer},
        address = {New York}
}

@book{RBioinf,
  author = {R. Gentleman},
  year = {2008},
  title = {R Programming for Bioinformatics},
  publisher = {CRC Press}
}

@Book{JMCBook,
  author = {J. M. Chambers},
  title = {Software for Data Analysis: Programming with {R}},
  year = {2008},
  publisher = {Springer},
  address = {New York}
}

@Book{BiocCaseStudies,
  author = {F. Hahne and W. Huber and R. Gentleman and S. Falcon},
  title = {Bioconductor Case Studies},
  publisher = {Springer},
  year = {2008},
  ADDRESS = {New York}
}



@article{Sanchez2004,
 journal = {Biotechnology Letters},
 year = {2004}, 
 volume = {26},
 pages = {403--7},
 title = {Bacillus subtilis transcriptional regulators interaction},
 author = {A. Sanchez and J. Olmos}
}

@article{Dayhoff:1978,
  title={{A model of evolutionary change in proteins}},
  author={Dayhoff, M.O. and Schwartz, R.M. and Orcutt, BC},
  journal={Atlas of Protein Sequence and Structure},
  volume=5,
  number={Suppl 3},
  pages={345--352},
  year=1978
}


@article{Altschul:1990,
   Author = {Altschul, S. F. and Gish, W. and Miller, W. and Myers,
                  E. W. and Lipman, D. J.},
   Year = {1990},
   Title = {Basic local alignment search tool},
   Journal = {J Mol Biol},
   Volume = {215},
   Number = {3},
   Pages = {403-10},
   Accession  = {2231712}
}


@article{Altschul:1997,
   Author = {Altschul, S. F. and Madden, T. L. and Schaffer, A. A. and
                  Zhang, J. and Zhang, Z. and Miller, W. and Lipman,
                  D. J.},
   Year = {1997},
   Title = {Gapped BLAST and PSI-BLAST: a new generation of protein
                  database search programs},
   Journal = {Nucleic Acids Res},
   Volume = {25},
   Number = {17},
   Pages = {3389-402}
}


@book{Gentleman:2005,
   Author = {Gentleman, R and Carey, V and Huber, W and Irizarry, R and Dudoit, S},
   Year = {2005},
   Title = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor},
   Publisher = {Springer},
   Series = {Statistics for Biology and Health},
   ISBN = {978-0-387-25146-2}, 
}

@incollection{Huber:2005,
   Author = {Huber, W and Irizarry, R and Gentleman, R},
   Title = {Preprocessing overview},
   BookTitle = {Bioinformatics and Computational Biology Solutions Using R and Bioconductor},
   Editor = {Gentleman, R and Carey, V and Huber, W and Irizarry, R and Dudoit, S},
   Series = {Statistics for Biology and Health},
   Publisher = {Springer},
   Pages = {3-12},
   Year = {2005} 
}


@article{Scholtens:2008,
   Author = {Scholtens, D. and Chiang, T. and Huber, W. and
                  Gentleman, R.},
   Year = {2008},
   Title = {Estimating node degree in bait-prey graphs.},
   Journal = {Bioinformatics},
   Volume = {24},
   Number = {2},
   Pages = {218-24}
}


@article{Hoefnagel:2002,
   Author = {Hoefnagel, MH. and Starrenburg, MJ. and Martens, DE. and
                  Hugenholtz, J. and Kleerebezem, M. and Van Swam II
                  and Bongers, R. and Westerhoff, HV. and Snoep, JL.},
   Year = {2002},
   Title = {Metabolic engineering of lactic acid bacteria, the combined approach: kinetic
modelling, metabolic control and experimental analysis.},
   Journal = {Microbiology},
   Volume = {148},
   Number = {4},
   Pages = {1003-13}
}


@article{LeNovere:2006,
   Author = {Le Novère, N. and Bornstein, B. and Broicher, A. and
                  Courtot, M. and Donizelli, M. and Dharuri, H. and Li, L. and
                  Sauro, H. and Schilstra, M. and Shapiro, B. and Snoep, JL. and Hucka, M.},
   Year = {2006},
   Title = {BioModels Database: a free, centralized database of curated, published,
quantitative kinetic models of biochemical and cellular systems.},
   Journal = {Nucleic Acids Res.},
   Volume = {34},
   Number = {Database issue},
   Pages = {D689-91}
}


@article{Castro:2008,
   Author = {Gama-Castro, S. et al},
   Year = {2008},
   Title = {RegulonDB (Version 6.0): gene regulation model of Escherichia coli K-12 
beyond transcription, active (experimental) annotated promoters and textpresso navigation.},
   Journal = {Nucleic Acids Res.},
   Volume = {36},
   Number = {Database issue},
   Pages = {D120-D124}
}

@article{Jensen:2009,
   Author = {Jensen, LJ. and Kuhn, M. and Stark, M. and Chaffron,
                  S. and Creevey, C. and Muller, J. and Doerks, T. and
                  Julien, P. and Roth, A. and Simonovic, M. and Bork,
                  P. and von Mering, C.},
   Year = {2009},
   Title = {STRING 8--a global view on proteins and their functional
                  interactions in 630 organisms.},
   Journal = {Nucleic Acids Res.},
   Volume = {37},
   Number = {Database issue},
   Pages = {D412-416}
}

@article{Castelo:2009,
   Author = {Castelo,R. and Roverato, A.},
   Year = {2009},
   Title = {Reverse engineering molecular regulatory networks from microarray data with
qp-graphs.},
   Journal = {J Comput Biol.},
   Volume = {16},
   Number = {2},
   Pages = {213-227}
}

@article{LeMeur:2008,
   Author = {Le Meur,N. and Gentleman, R.},
   Year = {2008},
   Title = {Modeling synthetic lethality.},
   Journal = {Genome Biol.},
   Volume = {9},
   Number = {9},
   Pages = {R135}
}

@Manual{Rref,
       title        = {R: A Language and Environment for Statistical
                       Computing},
       author       = {{R Development Core Team}},
       organization = {R Foundation for Statistical Computing},
       address      = {Vienna, Austria},
       year         = 2009,
       note         = {{ISBN} 3-900051-07-0},
       url          = {http://www.R-project.org}
     }


@article{Huber:2007,
   Author = {W. Huber and V. J. Carey and  L. Long and S. Falcon and R. Gentleman},
   Year = {2007},
   Title = {Graphs in molecular biology.},
   Journal = {BMC Bioinformatics},
   Volume = {8},
   Number = {6},
   Pages = {S8}
}

@incollection{graphviz,
    author = {J. Ellson and E.R. Gansner and E. Koutsofios and S.C.
                  North and G.  Woodhull},
    title = {Graphviz and Dynagraph -- Static and Dynamic Graph
                  Drawing Tools},
    booktitle = {Graph Drawing Software},
    year = {2004},
    editor = {M. Junger and P. Mutzel},
    pages = {127-148},
    publisher = {Springer-Verlag}
}

@INPROCEEDINGS{Sweave,
  AUTHOR = {Friedrich Leisch},
  TITLE = {Sweave: Dynamic Generation of Statistical Reports Using
                  Literate Data Analysis},
  BOOKTITLE = {Compstat 2002 --- Proceedings in Computational
                  Statistics},
  PAGES = {575--580},
  YEAR = 2002,
  EDITOR = {Wolfgang H{\"a}rdle and Bernd R{\"o}nz},
  PUBLISHER = {Physika Verlag, Heidelberg, Germany},
  NOTE = {ISBN 3-7908-1517-9},
  URL = {http://www.ci.tuwien.ac.at/~leisch/Sweave}
}

@article{GO:2000,
author = {{The Gene Ontology Consortium}}, 
title = {Gene ontology: tool for the unification of biology.}, 
year  = {2000},
Journal = {Nat. Genet.},
volume= {25},
number = {1},
pages = {25-9}
}


@article{Missiakas:1997,
author = {Missiakas, D. and Mayer, MP. and Lemaire, M. and Georgopoulos, C. and Raina, S.}, 
title = {Modulation of the Escherichia coli sigmaE (RpoE) heat-shock
                  transcription-factor activity by the RseA, RseB and
                  RseC proteins.}, 
year  = {1997},
Journal = {Mol. Microbiol},
volume= {24},
number = {2},
pages = {355-71}
}

@article{Hahne:2009,
author = {Hahne, F. and Le Meur, N. and  Brinkman, R.R and Ellis, B. and Haaland, P. and Sarkar, D. and Spidlen, J. and Strain, E. and Gentleman, R.},
title={flowCore: a Bioconductor package for high throughput flow cytometry.}, 
Journal = {BMC Bioinformatics}, 
year = {2009},
volume = {10},
pages = {106}
}

@article{Morgan2009,
author = {Morgan, M. and Anders, S. and Lawrence, M. and Aboyoun, P. and Pagès, H. and Gentleman, R.},
title = {ShortRead: a bioconductor package for input, quality assessment and exploration
of high-throughput sequence data.},
journal = {Bioinformatics},
year = {2009},
volume = {25},
number = {19},
pages = {2607-8}
}

@article{Boutros2006,
author = {Boutros, M. and Bras, LP. and Huber, W.},
title = {Analysis of cell-based RNAi screens.},
journal = {Genome Biol.},
year= {2006},
volume = {7},
number = {7},
pages = {R66}
}

@article{Gentleman2007,
author = {Gentleman, R. and Huber, W.},
title = {Making the most of high-throughput protein-interaction data.},
journal = {Genome Biol.}, 
year= {2007},
volume = {8},
number = {10},
pages = {112}
}

@article{Schuchhardt2000,
author = {Schuchhardt, J. and Beule, D. and Malik, A. and Wolski,
                  E. and Eickhoff, H. and Lehrach, H. and Herzel, H.},
title = {Normalization strategies for cDNA microarrays.},
journal = {Nucleic Acids Res.},
year= {2000},
volume = {28},
number = {10},
pages = {E47}
}


@article{Ishikawa2006,
author = {Ishikawa, S. and Kawai, Y. and Hiramatsu, K. and Kuwano, M. and Ogasawara, N.},
title = {A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during
progression of cell division in Bacillus subtilis.},
journal = {Mol Microbiol.}, 
year= {2006},
volume = {60},
number = {6},
pages = {1364-80}
}


@article{Chiang2007,
author = {Chiang, T. and Scholtens, D. and Sarkar, D. and Gentleman, R. and Huber, W.},
title = {Coverage and error models of protein-protein interaction data by directed graph analysis.},
journal = {Genome Biol.}, 
year= {2007},
volume = {8},
number = {9},
pages = {R186}
}


@article{Chiang2009,
author = {Chiang, T. and Scholtens, D.},
title = {A general pipeline for quality and statistical assessment of protein interaction 
data using R and Bioconductor.},
journal = {Nat Protoc.}, 
year= {2009},
volume = {4},
number = {4},
pages = {535-46}
}


@article{Bruckner2009,
author = {Brückner, A. and Polge, C. and Lentze, N. and Auerbach, D. and Schlattner, U.},
title = {Yeast two-hybrid, a powerful tool for systems biology.},
journal = {Int J Mol Sci.}, 
year= {2009},
volume = {10},
number = {6},
pages = {2763-88}
}

@article{Wingren2009,
author = {Wingren, C. and James, P. and Borrebaeck, CA.},
title = {Strategy for surveying the proteome using affinity proteomics and mass
spectrometry.},
journal = {Proteomics}, 
year= {2009},
volume = {9},
number = {6},
pages = {1511-7}
}

@article{Covert2004,
author = {Covert, MW. and Knight, EM. and Reed, JL. and Herrgard,
                  MJ. and Palsson, BO.},
title = {Integrating high-throughput and computational data elucidates
                  bacterial networks.},
journal = {Nature}, 
year= {2004},
volume = {429},
number = {6987},
pages = {92-6}
}


@article{Blattner1997,
author = {Blattner, FR. and Plunkett, G 3rd. and Bloch, CA. and Perna,
                  NT. and Burland, V. and Riley, M. and Collado-Vides,
                  J. and Glasner, JD. and Rode, CK. and Mayhew,
                  GF. and Gregor, J. and Davis, NW. and Kirkpatrick,
                  HA. and Goeden, MA. and Rose, DJ. and Mau, B. and
                  Shao, Y.},
title = {The Complete Genome Sequence of Escherichia coli K-12.},
journal = {Science}, 
year= {1997},
volume = {277},
number = {5331},
pages = {1453-62}
}

@article{ge2001,
author = {Ge, H. and Liu, Z. and Church, GM. and Vidal, M.},
title = {Correlation between transcriptome and interactome mapping
                  data from Saccharomyces cerevisiae.},
journal = {Nat Genet.}, 
year= {2001},
volume = {29},
number = {4},
pages = {482-6}
}


@article{Mootha2003,
author = {Mootha, VK. and Lindgren, CM. and Eriksson, KF. and
                  Subramanian, A. and Sihag, S. and Lehar, J. and
                  Puigserver, P. and Carlsson, E. and Ridderstrale,
                  M. and Laurila, E. and Houstis, N. and Daly,
                  MJ. and Patterson, N. and Mesirov, JP. and Golub,
                  TR. and Tamayo, P. and Spiegelman, B. and Lander,
                  ES. and Hirschhorn, JN. and Altshuler, D. and Groop,
                  LC.},
title = {PGC-1alpha-responsive genes involved in oxidative
                  phosphorylation are coordinately downregulated in
                  human diabetes.},
journal = {Nat Genet.}, 
year= {2003},
volume = {34},
number = {3},
pages = {267-73}
}


@article{Subramanian2005,
author = {Subramanian, A. and Tamayo, P. and Mootha, VK. and
                  Mukherjee, S. and Ebert, BL. and Gillette, MA. and
                  Paulovich, A. and Pomeroy, SL. and Golub, TR. and
                  Lander, ES. and Mesirov, JP.},
title = {Gene set enrichment analysis: a knowledge-based approach for
                  interpreting genome-wide expression profiles.},
journal = {Proc Natl Acad Sci U S A.}, 
year= {2005},
volume = {102},
number = {43},
pages = {15545-50}
}


@article{KEGG,
author = {Kanehisa, M. and Goto, S.},
title = {KEGG: kyoto encyclopedia of genes and genomes.},
journal = {Nucleic Acids Res.}, 
year= {2000},
volume = {28},
number = {1},
pages = {27-30}
}

@article{eisendle2006,
  title={The intracellular siderophore ferricrocin is involved in iron storage, oxidative-stress resistance, germination, and sexual development in Aspergillus nidulans.},
  author={Eisendle, M. and Schrettl, M. and Kragl, C. and Muller, D. and Illmer, P. and Haas, H.},
  journal={Eukaryotic Cell},
  volume={5},
  number={10},
  pages={1596},
  year={2006},
  publisher={Am Soc Microbiol}
}

@article{shannon2003,
  title={Cytoscape: a software environment for integrated models of
                  biomolecular interaction networks.},
  author={Shannon, P. and Markiel, A. and Ozier, O. and Baliga, N.S. and Wang, J.T. and Ramage, D. and Amin, N. and Schwikowski, B. and Ideker, T.},
  journal={Genome research},
  volume={13},
  number={11},
  pages={2498},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}


@article{iuchi1988,
  title={arcA(dye), a global regulatory gene in Escherichia coli
                  mediating repression of enzymes in aerobic pathways.},
  author={Iuchi, S. and Lin, ECC},
  journal={Proceedings of the National Academy of Sciences, USA},
  volume={85},
  number={6},
  pages={1888-92},
  year={1988},
  publisher={National Acad Sciences}
}

@article{salmon2003,
  title={Global gene expression profiling in Escherichia coli K12.The
                  effects of oxygen availability and FNR.},
  author={Salmon, K. and Hung, S. and Mekjian, K. and Baldi, P. and
                  Hatfield, G. and Gunsalus, R.P.},
  journal={Journal of Biological Chemistry},
  volume={278},
  number={32},
  pages={29837-55},
  year={2003},
  publisher={ASBMB}
}

@article{correnti2002,
  title={Dam-dependent phase variation of Ag 43 in Escherichia coli
                  is altered in a seqA mutant.},
  author={Correnti, J. and Munster, V. and Chan, T. and Woude, M.},
  journal={Molecular Microbiology},
  volume={44},
  number={2},
  pages={521-32},
  year={2002}
}

@article{chen2008,
  title={A novel OxyR sensor and regulator of hydrogen peroxide stress
                  with one cysteine residue in Deinococcus
                  radiodurans.},
  author={Chen, H. and Xu, G. and Zhao, Y. and Tian, B. and Lu, H. and
                  Yu, X. and Xu, Z. and Ying, N. and Hu, S. and Hua,
                  Y.},
  journal={PLoS ONE},
  volume={3},
  number={2},
  pages={e1602},
  year={2008},
  publisher={Public Library of Science}
}


@article{brondsted1996,
  title={{Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli}},
  author={Brondsted, L. and Atlung, T.},
  journal={Journal of bacteriology},
  volume={178},
  number={6},
  pages={1556},
  year={1996},
  publisher={Am Soc Microbiol}
}

@article{falcon2007,
  title={{Using GOstats to test gene lists for GO term association}},
  author={Falcon, S. and Gentleman, R.},
  journal={Bioinformatics},
  volume={23},
  number={2},
  pages={257-258},
  year={2007},
  publisher={Oxford Univ Press}
}
