| Ghosh Dastidar R, et al. (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30 |
| 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 |
| 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 |
| 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 |
| Ostrow AZ, et al. (2014) Fkh1 and Fkh2 Bind Multiple Chromosomal Elements in the S. cerevisiae Genome with Distinct Specificities and Cell Cycle Dynamics. PLoS One 9(2):e87647 |
| Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8 |
| Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87 |
| Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103 |
| Lavoie H, et al. (2010) Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol 8(3):e1000329 |
| On T, et al. (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89 |
| 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 |
| Pondugula S, et al. (2009) Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins. Mol Cell Biol 29(18):4891-905 |
| 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 |
| 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 |
| 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 |
| 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 |
| Ercan S, et al. (2005) Yeast recombination enhancer is stimulated by transcription activation. Mol Cell Biol 25(18):7976-87 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Ward LD and Bussemaker HJ (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24(13):i165-71 |
| 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 |
| Gordan R, et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19(11):2090-100 |
| McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Koranda M, et al. (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406(6791):94-8 |
| 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 |
| Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8 |
| Erb I and van Nimwegen E (2011) Transcription factor binding site positioning in yeast: proximal promoter motifs characterize tata-less promoters. PLoS One 6(9):e24279 |
| Murakami H, et al. (2010) Regulation of yeast forkhead transcription factors and FoxM1 by cyclin-dependent and polo-like kinases. Cell Cycle 9(16):3233-42 |
| 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 |
| Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7 |
| Shapira M, et al. (2004) Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell 15(12):5659-69 |
| Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708 |
| Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56 |
| Hollenhorst PC, et al. (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev 15(18):2445-56 |
| 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 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146 |
| Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94 |
| Sekiya M, et al. (2009) Transcription factors of M-phase cyclin CLB2 in the yeast cell wall integrity checkpoint. Genes Genet Syst 84(4):269-76 |
| 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 |
| Breeden LL (2000) Cyclin transcription: Timing is everything. Curr Biol 10(16):R586-8 |
| Morozov AV and Siggia ED (2007) Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A 104(17):7068-73 |