The 21 papers which experimentally study the biological roles of both TFs of the PCTFP (Stb1-Ndd1)
Chang EJ, et al. (2007) Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One 2(7):e656
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
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
Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64
Koivomagi M, et al. (2011) Dynamics of Cdk1 Substrate Specificity during the Cell Cycle. Mol Cell 42(5):610-23
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
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
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Koivomagi M, et al. (2013) Multisite phosphorylation networks as signal processors for Cdk1. Nat Struct Mol Biol 20(12):1415-24
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458
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
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
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
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
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