The 69 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi5-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
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
Imoto S, et al. (2003) Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf 2():104-13
Kumar R, et al. (2000) Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol 10(15):896-906
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Pic A, et al. (2000) The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF. EMBO J 19(14):3750-61
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
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Garcia-Bustos JF, et al. (1991) Nuclear import substrates compete for a limited number of binding sites. Evidence for different classes of yeast nuclear import receptors. J Biol Chem 266(33):22303-6
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
Vinod PK, et al. (2011) Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles. J R Soc Interface 8(61):1128-41
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
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
Lim FL, et al. (2003) Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes. Mol Cell Biol 23(2):450-61
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
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
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
Higa CH, et al. (2011) Constraint-based analysis of gene interactions using restricted boolean networks and time-series data. BMC Proc 5 Suppl 2():S5
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
Gordan R, et al. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 12(12):R125
Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35
Tan M, et al. (2010) Scalable approach for effective control of gene regulatory networks. Artif Intell Med 48(1):51-59
Mangla K, et al. (2010) Timing robustness in the budding and fission yeast cell cycles. PLoS One 5(2):e8906
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94
Wang H, et al. (1994) Genetic interactions between SIN3 mutations and the Saccharomyces cerevisiae transcriptional activators encoded by MCM1, STE12, and SWI1. Mol Gen Genet 245(6):675-85
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35
Thompson EG and Galitski T (2012) Quantifying and analyzing the network basis of genetic complexity. PLoS Comput Biol 8(7):e1002583
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
Nachman I, et al. (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 Suppl 1:I248-I256
Wang G, et al. (2010) Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A 107(23):10478-83
Liu XS, et al. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 20(8):835-9
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85
Higa CH, et al. (2013) Growing seed genes from time series data and thresholded Boolean networks with perturbation. IEEE/ACM Trans Comput Biol Bioinform 10(1):37-49
Chen KC, et al. (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15(8):3841-62
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
Ay F, et al. (2009) Scalable steady state analysis of boolean biological regulatory networks. PLoS One 4(12):e7992
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
Poirel CL, et al. (2013) Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol 20(5):409-18
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
Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87
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
Gallo CA, et al. (2011) Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers. BMC Bioinformatics 12(1):123
Haber JE (2012) Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae. Genetics 191(1):33-64
Hvidsten TR, et al. (2005) Discovering regulatory binding-site modules using rule-based learning. Genome Res 15(6):856-66
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
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
Althoefer H, et al. (1995) Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae. Mol Cell Biol 15(11):5917-28
Keles S, et al. (2004) Regulatory motif finding by logic regression. Bioinformatics 20(16):2799-811
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
Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Moriya H, et al. (2006) In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2(7):e111
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
Verdicchio MP and Kim S (2011) Identifying targets for intervention by analyzing basins of attraction. Pac Symp Biocomput ():350-61
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
Darieva Z, et al. (2006) Polo kinase controls cell-cycle-dependent transcription by targeting a coactivator protein. Nature 444(7118):494-8
Lydall D, et al. (1991) A new role for MCM1 in yeast: cell cycle regulation of SW15 transcription. Genes Dev 5(12B):2405-19
Freire P, et al. (2012) Interplay of transcriptional and proteolytic regulation in driving robust cell cycle progression. Mol Biosyst 8(3):863-70