The 36 papers which experimentally study the biological roles of both TFs of the PCTFP (Swi4-Stb1)
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8
Alberghina L, et al. (2009) Molecular networks and system-level properties. J Biotechnol 144(3):224-33
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
Costanzo M, et al. (2003) G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol 23(14):5064-77
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
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
Takahata S, et al. (2011) Repressive chromatin affects factor binding at yeast HO (homothallic switching) promoter. J Biol Chem 286(40):34809-19
Ho Y, et al. (1999) Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol 19(8):5267-78
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92
Ferrezuelo F, et al. (2012) The critical size is set at a single-cell level by growth rate to attain homeostasis and adaptation. Nat Commun 3():1012
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458
Chang EJ, et al. (2007) Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One 2(7):e656
Eriksson PR, et al. (2012) Regulation of histone gene expression in budding yeast. Genetics 191(1):7-20
Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414
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
de Bruin RA, et al. (2008) Stb1 collaborates with other regulators to modulate the G1-specific transcriptional circuit. Mol Cell Biol 28(22):6919-28
Costanzo M, et al. (2004) CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell 117(7):899-913
Poirel CL, et al. (2013) Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol 20(5):409-18
Wang RS, et al. (2007) Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics 23(22):3056-3064
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
Banerjee N and Zhang MQ (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23):7024-31
Lai FJ, et al. (2014) A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol 8 Suppl 4():S9
Wang H, et al. (2009) Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets. PLoS Biol 7(9):e1000189
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Stillman DJ (2013) Dancing the cell cycle two-step: regulation of yeast G1-cell-cycle genes by chromatin structure. Trends Biochem Sci 38(9):467-75
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
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
Takahata S, et al. (2009) The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters. EMBO J 28(21):3378-89
Alarcon T and Tindall MJ (2007) Modelling cell growth and its modulation of the G1/S transition. Bull Math Biol 69(1):197-214