| 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 |
| 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 |
| Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
| Yang YL, et al. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 6():90 |
| Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8 |
| 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 |
| Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Novo M, et al. (2013) Genome-Wide Study of the Adaptation of Saccharomyces cerevisiae to the Early Stages of Wine Fermentation. PLoS One 8(9):e74086 |
| 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 |
| de Lichtenberg U, et al. (2005) New weakly expressed cell cycle-regulated genes in yeast. Yeast 22(15):1191-201 |
| Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6 |
| Nachman I, et al. (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 Suppl 1:I248-I256 |
| Nguyen Ba AN, et al. (2014) Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Comput Biol 10(12):e1003977 |
| 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 |
| Voth WP, et al. (2007) Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J 26(20):4324-34 |
| Darieva Z, et al. (2012) Protein kinase C regulates late cell cycle-dependent gene expression. Mol Cell Biol 32(22):4651-61 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| 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 |
| 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 |
| Haber JE (2012) Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae. Genetics 191(1):33-64 |
| McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85 |
| Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Zhu G, et al. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406(6791):90-4 |
| 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 |
| 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 |
| 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 |
| Ye C, et al. (2009) Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol 5(3):e1000311 |
| Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708 |
| Postnikoff SD and Harkness TA (2012) Mechanistic insights into aging, cell-cycle progression, and stress response. Front Physiol 3():183 |
| Goh WS, et al. (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6(1):e1000649 |
| 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 |
| 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 |
| Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94 |
| Fernandez MA, et al. (2012) Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species. Nucleic Acids Res 40(7):2823-32 |
| Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet () |