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

@INPROCEEDINGS{Bender2008,
  author = {Christian Bender and Holger Fr\"{o}hlich and Marc Johannes and Tim Bei{\ss}barth},
  title = {Extending pathways with inferred regulatory interactions from microarray
	data and protein domain signatures},
  booktitle = {CAMDA: Critical Assessment of Microarray Data Analysis},
  year = {2008},
  pages = {48-52},
}

@ARTICLE{Bender2010,
  author = {Christian Bender and Frauke Henjes and Holger Fr\"{o}hlich and Stefan
	Wiemann and Ulrike Korf and Tim Bei{\ss}barth},
  title = {Dynamic deterministic effects propagation networks: learning signalling
	pathways from longitudinal protein array data.},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {i596--i602},
  number = {18},
  month = {Sep},
  doi = {10.1093/bioinformatics/btq385},
  institution = {Department of Molecular Genome Analysis, German Cancer Research Center,
	69120 Heidelberg, Department of Algorithmic Bioinformatics, Bonn-Aachen
	International Center for IT, 53113 Bonn and Department of Medical
	Statistics, University of Göttingen, 37099 Göttingen, Germany.},
  language = {eng},
  medline-pst = {ppublish},
  pmid = {20823327},
  url = {http://dx.doi.org/10.1093/bioinformatics/btq385}
}
@PHDTHESIS{Bender2011,
  author = {Christian Bender},
  title = {Systematic analysis of time resolved high-throughput data using stochastic
    network inference methods},
  school = {Faculty of Biology at University of Heidelberg},
  year = {2011},
  address = {Im Neuenheimer Feld 580, 69121 Heidelberg},
  month = {May}
}
@UNPUBLISHED{Bender2011a,
  author = {Christian Bender and Silvia v.d. Heyde and Frauke Henjes and Stefan
    Wiemann and Ulrike Korf and Tim Bei{\ss}barth},
  title = {Inferring signalling networks from longitudinal data using sampling
    based approaches in the R package 'ddepn'},
  note = {accepted at BMC Bioinformatics, 2011},
  month = {July},
  year = {2011},
  folder = {NONE},
  num = {622},
  owner = {benderc},
  timestamp = {2011.02.15}
}

@Article{Bioconductor2004,
    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 Biology},
    volume = {5},
    year = {2004},
    pages = {R80},
    url = {http://genomebiology.com/2004/5/10/R80},
  }
@ARTICLE{Froehlich2007,
  author = {Holger Fr\"{o}hlich and Mark Fellmann and Holger S\"{u}ltmann and Annemarie
    Poustka and Tim Bei{\ss}barth},
  title = {Large scale statistical inference of signaling pathways from RNAi
    and microarray data.},
  journal = {BMC Bioinformatics},
  year = {2007},
  volume = {8},
  pages = {386},
  number = {11},
  institution = {German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120
    Heidelberg, Germany. h.froehlich@dkfz-heidelberg.de},
  pii = {1471-2105-8-386},
  pmid = {17937790},
}
@ARTICLE{Froehlich2008,
  author = {Holger Fr\"{o}hlich and Mark Fellmann and Holger S\"{u}ltmann and Annemarie
	Poustka and Tim Bei{\ss}barth},
  title = {Estimating Large Scale Signaling Networks through Nested Effect Models
	with Intervention Effects from Microarray Data.},
  journal = {Bioinformatics},
  year = {2008},
  volume = {24},
  pages = {2650-2656},
  number = {22},
  month = {Jan},
  institution = {German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120
	Heidelberg, German.},
  pii = {btm634},
  pmid = {18227117},
}
@ARTICLE{Goh2001,
  author = {K. I. Goh and B. Kahng and D. Kim},
  title = {Universal behavior of load distribution in scale-free networks.},
  journal = {Phys Rev Lett},
  year = {2001},
  volume = {87},
  pages = {278701},
  number = {27 Pt 1},
  month = {Dec},
  institution = {School of Physics and Center for Theoretical Physics, Seoul National
	University, Seoul 151-747, Korea.},
  keywords = {Information Services; Models, Biological; Models, Theoretical},
  pmid = {11800921},
}

@MISC{Kamimura,
  author = {Kamimura, Takeshi and Shimodaira, Hidetoshi},
  title = {A Scale-free Prior over Graph Structures for Bayesian Inference of
	Gene Networks},
  howpublished = {Online},
  keywords = {Scale-free random graphs, Power law, Bayesian Inference, Gaussian
	graphical model, Markov chain Monte Carlo, microarray, gene network},
}
  author = {Kanehisa, M. and Araki, M. and Goto, S. and Hattori, M. and Hirakawa,
    M. and Itoh, M. and Katayama, T. and Kawashima, S. and Okuda, S.
    and Tokimatsu, T. and Yamanishi, Y.},

@ARTICLE{Kanehisa2008KEGG,
  author = {M. Kanehisa and M. Araki and S. Goto and M. Hattori and M. Hirakawa and 
    M. Itoh and T. Katayama and S. Kawashima and S. Okuda and T. Tokimatsu and
    Y. Yamanishi},
  title = {{KEGG} for linking genomes to life and the environment},
  journal = {Nucleic Acids Res.},
  year = {2008},
  volume = {36},
  pages = {D480 - D484},
}
@ARTICLE{Lee2005,
  author = {Lee, D-S and Goh, K-I and Kahng, B and Kim, D},
  title = {Scale-free random graphs and Potts model},
  journal = {Pramana - journal of physics},
  year = {2005},
  volume = {64},
  pages = {1149--1159},
  number = {6},
  month = {June},
}
@Manual{Rproject2010,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2010},
  note = {{ISBN} 3-900051-07-0},
  url = {http://www.R-project.org},
}
@ARTICLE{Spellman1998,
  author = {P. T. Spellman and G. Sherlock and M. Q. Zhang and V. R. Iyer and
	K. Anders and M. B. Eisen and P. O. Brown and D. Botstein and B.
	Futcher},
  title = {Comprehensive identification of cell cycle-regulated genes of the
	yeast Saccharomyces cerevisiae by microarray hybridization.},
  journal = {Mol Biol Cell},
  year = {1998},
  volume = {9},
  pages = {3273--3297},
  number = {12},
  month = {Dec},
  institution = {Department of Genetics, Stanford University Medical Center, Stanford,
	California 94306-5120, USA.},
  keywords = {Base Sequence; Binding Sites, genetics; Cell Cycle, genetics; Cyclin
	B; Cyclins, genetics; DNA Primers, genetics; DNA Repair, genetics;
	DNA Replication, genetics; DNA, Fungal, genetics/metabolism; Fungal
	Proteins, genetics; Gene Expression Regulation, Fungal; Genes, Fungal;
	Multigene Family; Nucleic Acid Hybridization, methods; RNA, Fungal,
	genetics/metabolism; RNA, Messenger, genetics/metabolism; Saccharomyces
	cerevisiae Proteins; Saccharomyces cerevisiae, cytology/genetics/metabolism;
	Transcription, Genetic},
  language = {eng},
  medline-pst = {ppublish},
  pmid = {9843569},
}

@ARTICLE{Werhli2007,
  author = {Adriano V. Werhli and Dirk Husmeier},
  title = {Reconstructing gene regulatory networks with bayesian networks by
	combining expression data with multiple sources of prior knowledge.},
  journal = {Stat Appl Genet Mol Biol},
  year = {2007},
  volume = {6},
  pages = {Article15},
  doi = {10.2202/1544-6115.1282},
  institution = { Statistics Scotland (BioSS) and Edinburgh University, UK. adriano@bioss.ac.uk},
  keywords = {Bayes Theorem; Gene Expression; Genes, Regulator; Immunoprecipitation;
	Markov Chains; Monte Carlo Method; Probability},
}











@article{blank,
	author  = {}, 
	title   = {},
	journal = {}, 
	year  = {},
	  month = {}, 
	  volume= {}, 
	  number= {}, 
	  pages = {},
	  note  = {} 
}	

% Article within a journal
@ARTICLE{koon,
	author  = {Koonin, E V and Altschul, S F and P Bork}, 
	title   = {BRCA1 protein products: functional motifs}, 
	journal = {Nat Genet}, 
	year    = {1996},
	volume  = {13}, 
	pages   = {266-267}
}	

% 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{xjon,
	author    = {X Jones}, 
	title     = {Zeolites and synthetic mechanisms},
	booktitle = {Proceedings of the First National Conference on 
		     Porous Sieves: 27-30 June 1996; Baltimore},
	year      = {1996},
	  editor  = {Y Smith}, 
	  pages   = {16-27},
	  organization  = {Stoneham: Butterworth-Heinemann}
}	

%%%%%%%%
%  Book chapter, or article within a book
%
@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} 
}	

%%%%%%%%
% 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{marg,
	author    = {L Margulis}, 
	title     = {Origin of Eukaryotic Cells},
	publisher = {Yale University Press}, 
	year      = {1970},
	address   = {New Haven} 
}



%%%%%%%%
% 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{advi,
	  title   = {Annual Report}, 
	    organization  = {Advisory Committee on Genetic Modification}, 
	    address = {London},
	    year    = {1999}
}


%%%%%%%%
% 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{mouse,
	title  = {The Mouse Tumor Biology Database},
	url = {http://tumor.informatics.jax.org/cancer_links.html}
}


