The 49 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi6-Mcm1)
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
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
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
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Zhao XM, et al. (2008) Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 36(9):e48
Cote P, et al. (2009) Transcriptional analysis of the Candida albicans cell cycle. Mol Biol Cell 20(14):3363-73
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Gormley M, et al. (2011) An integrated framework to model cellular phenotype as a component of biochemical networks. Adv Bioinformatics 2011():608295
Jung PP, et al. (2011) Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae. BMC Genomics 12(1):331
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
Ferrezuelo F, et al. (2009) Bck2 is a phase-independent activator of cell cycle-regulated genes in yeast. Cell Cycle 8(2):239-52
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Haber JE (2012) Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae. Genetics 191(1):33-64
Mathiasen DP and Lisby M (2014) Cell cycle regulation of homologous recombination in Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):172-84
Lyu S (2009) Combining boolean method with delay times for determining behaviors of biological networks. Conf Proc IEEE Eng Med Biol Soc 1():4884-7
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
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
Alter O and Golub GH (2004) Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci U S A 101(47):16577-82
Zanders ED (2000) Gene expression analysis as an aid to the identification of drug targets. Pharmacogenomics 1(4):375-84
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94
Yu X, et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res 34(3):917-27
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
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
Zhao Y, et al. (2008) Development of a Novel Oligonucleotide Array-Based Transcription Factor Assay Platform for Genome-Wide Active Transcription Factor Profiling in Saccharomyces cerevisiae. J Proteome Res 7(3):1315-1325
Wang G, et al. (2010) Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A 107(23):10478-83
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
Lau KY, et al. (2007) Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys Rev E Stat Nonlin Soft Matter Phys 75(5 Pt 1):051907
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146
Poirel CL, et al. (2013) Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol 20(5):409-18
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
Braunewell S and Bornholdt S (2007) Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. J Theor Biol 245(4):638-43
Gallo CA, et al. (2011) Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers. BMC Bioinformatics 12(1):123
Wang X, et al. (2011) Nucleosomes and the accessibility problem. Trends Genet 27(12):487-92
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
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
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Moriya H, et al. (2006) In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2(7):e111
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6
Verdicchio MP and Kim S (2011) Identifying targets for intervention by analyzing basins of attraction. Pac Symp Biocomput ():350-61
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
Wang RS, et al. (2007) Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics 23(22):3056-3064