| 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 | 
        
                
            | 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 | 
        
                
            | 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 | 
        
                
            | Arnett DR, et al. (2008) A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol Cell Proteomics 7(11):2090-106 | 
        
                
            | 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 | 
        
                
            | Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 | 
        
                
            | 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 | 
        
                
            | Scrimale T, et al. (2009) The Unfolded Protein Response Is Induced by the Cell Wall Integrity Mitogen-activated Protein Kinase Signaling Cascade and Is Required for Cell Wall Integrity in Saccharomyces cerevisiae. Mol Biol Cell 20(1):164-75 | 
        
                
            | 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 | 
        
                
            | Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64 | 
        
                
            | 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 | 
        
                
            | Enserink JM and Kolodner RD (2010) An overview of Cdk1-controlled targets and processes. Cell Div 5():11 | 
        
                
            | 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 | 
        
                
            | 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 | 
        
                
            | Koivomagi M, et al. (2011) Dynamics of Cdk1 Substrate Specificity during the Cell Cycle. Mol Cell 42(5):610-23 | 
        
                
            | 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 | 
        
                
            | Eser U, et al. (2011) Commitment to a Cellular Transition Precedes Genome-wide Transcriptional Change. Mol Cell 43(4):515-27 | 
        
                
            | Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414 | 
        
                
            | 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 |