The 45 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi5-Ndd1)
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
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
Loy CJ, et al. (1999) NDD1, a high-dosage suppressor of cdc28-1N, is essential for expression of a subset of late-S-phase-specific genes in Saccharomyces cerevisiae. Mol Cell Biol 19(5):3312-27
Bristow SL, et al. (2014) Cell cycle-regulated transcription: effectively using a genomics toolbox. Methods Mol Biol 1170():3-27
Yang YL, et al. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 6():90
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
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Koivomagi M, et al. (2013) Multisite phosphorylation networks as signal processors for Cdk1. Nat Struct Mol Biol 20(12):1415-24
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
Gandhi SJ, et al. (2011) Transcription of functionally related constitutive genes is not coordinated. Nat Struct Mol Biol 18(1):27-34
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
Darieva Z, et al. (2012) Protein kinase C regulates late cell cycle-dependent gene expression. Mol Cell Biol 32(22):4651-61
Katzir Y, et al. (2013) Dynamics of the cell-cycle network under genome-rewiring perturbations. Phys Biol 10(6):066001
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
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
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
Petti AA and Church GM (2005) A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res 15(9):1298-306
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
Chang EJ, et al. (2007) Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One 2(7):e656
Moses AM, et al. (2007) Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol 8(2):R23
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
Darieva Z, et al. (2006) Polo kinase controls cell-cycle-dependent transcription by targeting a coactivator protein. Nature 444(7118):494-8
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
de Lichtenberg U, et al. (2005) New weakly expressed cell cycle-regulated genes in yeast. Yeast 22(15):1191-201
Enserink JM and Kolodner RD (2010) An overview of Cdk1-controlled targets and processes. Cell Div 5():11
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
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
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet ()