
@article{miller:2011,
author = {Miller, C. and Schwalb, B. and Maier, K. and Schulz, D. and Duemcke, S. and Zacher, B. and Mayer, A. and Sydow, J. and Marcinowski, L. and Dolken, L. and Martin, D. E. and Tresch, A. and Cramer, P.},
title = {Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.},
journal = {Mol Syst Biol},
year = {2011},
volume = {7},
number = {},
pages = {458},
}

%% transcription factor annotation
@article{fraenkel:2006,
author = {MacIsaac, K. D. and Wang, T. and Gordon, D. B. and Gifford, D. K. and Stormo, G. D. and Fraenkel, E.},
title = {An improved map of conserved regulatory sites for Saccharomyces cerevisiae.},
journal = {BMC Bioinformatics},
year = {2006},
volume = {7},
number = {},
pages = {113},
}

%% nr mRNAs
@article{zenklusen:2008,
author = {Zenklusen, D. and Larson, D. R. and Singer, R. H.},
title = {Single-RNA counting reveals alternative modes of gene expression in yeast.},
journal = {Nat Struct Mol Biol},
year = {2008},
volume = {15},
number = {12},
pages = {1263--1271},
}

%% Rp-genes
@article{nakao:2004,
    author = {Nakao, Akihiro and Yoshihama, Maki and Kenmochi, Naoya},
    journal = {Nucleic acids research},
    month = {January},
    number = {Database issue},
    title = {{RPG: the Ribosomal Protein Gene database.}},
    volume = {32},
    year = {2004}
}

%% RiBi genes
@article{jorgensen:2004,
    author = {Jorgensen, Paul and Rupe\r{A}!`, Ivan and Sharom, Jeffrey R. and Schneper, Lisa and Broach, James R. and Tyers, Mike},
    journal = {Genes \& Development},
    month = {October},
    number = {20},
    pages = {2491--2505},
    title = {{A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size}},
    volume = {18},
    year = {2004}
}

%% stress vector genes
@article{ihmels:2002,
    author = {Ihmels, Jan and Friedlander, Gilgi and Bergmann, Sven and Sarig, Ofer and Ziv, Yaniv and Barkai, Naama},
    journal = {Nature genetics},
    month = {August},
    number = {4},
    pages = {370--377},
    title = {{Revealing modular organization in the yeast transcriptional network.}},
    volume = {31},
    year = {2002}
}

@article{sgd,
author = {Cherry, J. M. and Adler, C. and Ball, C. and Chervitz, S. A. and Dwight, S. S. and Hester, E. T. and Jia, Y. and Juvik, G. and Roe, T. and Schroeder, M. and Weng, S. and Botstein, D.},
title = {SGD: Saccharomyces Genome Database.},
journal = {Nucleic Acids Res},
year = {1998},
volume = {26},
number = {1},
pages = {73--79},
}

@article{schwalb:2011,
    abstract = {{Create lots of colorful plots in a plethora of variations.}},
    author = {Schwalb, Bjoern and Tresch, Achim and Francois, Romain},
    journal = {The Comprehensive R Archive Network},
    title = {{LSD Lots of Superior Depictions}},
    url = {http://cran.r-project.org/web/packages/LSD/index.html},
    year = {2011}
}

@article{doelken:2008,
author = {Doelken, L. and Ruzsics, Z. and Raedle, B. and Friedel, C. C. and Zimmer, R. and Mages, J. and Hoffmann, R. and Dickinson, P. and Forster, T. and Ghazal, P. and Koszinowski, U. H.},
title = {High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.},
journal = {RNA},
year = {2008},
volume = {14},
number = {9},
pages = {1959--1972},
}

