Vohradska E and Vohradsky J (2011) Virtual mutagenesis of the yeast cyclins genetic network reveals complex dynamics of transcriptional control networks. PLoS One 6(4):e18827 |
Haase SB and Wittenberg C (2014) Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics 196(1):65-90 |
Reynolds D, et al. (2003) Recruitment of Thr 319-phosphorylated Ndd1p to the FHA domain of Fkh2p requires Clb kinase activity: a mechanism for CLB cluster gene activation. Genes Dev 17(14):1789-802 |
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169 |
Dyczkowski J and Vingron M (2005) Comparative analysis of cell cycle regulated genes in eukaryotes. Genome Inform Ser Workshop Genome Inform 16(1):125-31 |
Edenberg ER, et al. (2014) Rad53 downregulates mitotic gene transcription by inhibiting the transcriptional activator ndd1. Mol Cell Biol 34(4):725-38 |
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94 |
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
Wittenberg C and Reed SI (2005) Cell cycle-dependent transcription in yeast: promoters, transcription factors, and transcriptomes. Oncogene 24(17):2746-55 |
Yang YL, et al. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 6():90 |
Ostrow AZ, et al. (2014) Fkh1 and Fkh2 Bind Multiple Chromosomal Elements in the S. cerevisiae Genome with Distinct Specificities and Cell Cycle Dynamics. PLoS One 9(2):e87647 |
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8 |
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522 |
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421 |
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103 |
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146 |
Shapira M, et al. (2004) Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell 15(12):5659-69 |
Chen T and Li F (2009) Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data. Int J Bioinform Res Appl 5(6):625-46 |
Sun K, et al. (2002) Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer. Genes Dev 16(16):2085-96 |
Yelamanchi SK, et al. (2014) Genotoxic Stress Prevents Ndd1-Dependent Transcriptional Activation of G2/M-Specific Genes in Saccharomyces cerevisiae. Mol Cell Biol 34(4):711-24 |
Goh WS, et al. (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6(1):e1000649 |
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414 |
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94 |
Darieva Z, et al. (2006) Polo kinase controls cell-cycle-dependent transcription by targeting a coactivator protein. Nature 444(7118):494-8 |
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9 |
Darieva Z, et al. (2003) Cell cycle-regulated transcription through the FHA domain of Fkh2p and the coactivator Ndd1p. Curr Biol 13(19):1740-5 |
Negishi T and Ohya Y (2010) The cell wall integrity checkpoint: coordination between cell wall synthesis and the cell cycle. Yeast 27(8):513-9 |
To CC and Vohradsky J (2010) Measurement variation determines the gene network topology reconstructed from experimental data: a case study of the yeast cyclin network. FASEB J 24(9):3468-78 |
Huang SS and Fraenkel E (2012) Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple "-Omics" Datasets. Methods Cell Biol 110():57-80 |
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56 |
Manke T, et al. (2003) Correlating protein-DNA and protein-protein interaction networks. J Mol Biol 333(1):75-85 |
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6 |
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85 |
Koranda M, et al. (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406(6791):94-8 |
Asif HM and Sanguinetti G (2013) Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks. Stat Appl Genet Mol Biol 12(5):545-57 |
Postnikoff SD and Harkness TA (2012) Mechanistic insights into aging, cell-cycle progression, and stress response. Front Physiol 3():183 |
Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64 |
Veis J, et al. (2007) Activation of the G2/M-Specific Gene CLB2 Requires Multiple Cell Cycle Signals. Mol Cell Biol 27(23):8364-8373 |
Murakami H, et al. (2010) Regulation of yeast forkhead transcription factors and FoxM1 by cyclin-dependent and polo-like kinases. Cell Cycle 9(16):3233-42 |
Yu H and Gerstein M (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31 |
Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87 |
Banerjee N and Zhang MQ (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23):7024-31 |
Enserink JM and Kolodner RD (2010) An overview of Cdk1-controlled targets and processes. Cell Div 5():11 |
Breeden LL (2000) Cyclin transcription: Timing is everything. Curr Biol 10(16):R586-8 |
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708 |
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8 |
Pic-Taylor A, et al. (2004) Regulation of cell cycle-specific gene expression through cyclin-dependent kinase-mediated phosphorylation of the forkhead transcription factor Fkh2p. Mol Cell Biol 24(22):10036-46 |
Tuglus C and van der Laan MJ (2011) Repeated measures semiparametric regression using targeted maximum likelihood methodology with application to transcription factor activity discovery. Stat Appl Genet Mol Biol 10(1):Article2 |
Zhu Z, et al. (2002) Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol 318(1):71-81 |
Sherriff JA, et al. (2007) The Isw2 chromatin-remodeling ATPase cooperates with the Fkh2 transcription factor to repress transcription of the B-type cyclin gene CLB2. Mol Cell Biol 27(8):2848-60 |
Futcher B (2000) Microarrays and cell cycle transcription in yeast. Curr Opin Cell Biol 12(6):710-5 |
Pramila T, et al. (2006) The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev 20(16):2266-78 |
Manioudaki ME and Poirazi P (2013) Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet 4():110 |
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet () |
Negishi T, et al. (2016) The Late S-phase Transcription Factor Hcm1 is Regulated through Phosphorylation by the Cell Wall Integrity Checkpoint. Mol Cell Biol () |