| Ghosh Dastidar R, et al. (2012) The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Cell Biosci 2(1):30 |
| Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Contador CA, et al. (2011) Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae. Biotechnol Prog 27(4):925-36 |
| Kresnowati MT, et al. (2006) When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol Syst Biol 2():49 |
| 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 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| 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 |
| 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 |
| Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414 |
| 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 |
| Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001 |
| Pan J, et al. (2011) A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation. Cell 144(5):719-31 |
| 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 |
| Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
| 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 |
| Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74 |
| Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421 |
| 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 |
| Gordan R, et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19(11):2090-100 |
| Emmert-Streib F and Dehmer M (2009) Predicting cell cycle regulated genes by causal interactions. PLoS One 4(8):e6633 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| 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 |
| 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 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| 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 |
| Tuch BB, et al. (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol 6(2):e38 |