| van den Brink J, et al. (2008) New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess. BMC Genomics 9:100 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Mak HC, et al. (2009) Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res 19(6):1014-25 |
| Fondrat C and Kalogeropoulos A (1996) Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. Comput Appl Biosci 12(5):363-74 |
| 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 |
| 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 |
| Shah AN, et al. (2011) Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance. Physiol Genomics 43(14):855-72 |
| Chua G, et al. (2006) Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A 103(32):12045-50 |
| Elemento O, et al. (2007) A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types. Mol Cell 28(2):337-50 |
| Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001 |
| 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 |
| Hughes JD, et al. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296(5):1205-14 |
| Zeng T and Li J (2010) Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways. Nucleic Acids Res 38(1):e1 |
| Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421 |
| Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414 |
| Leyfer D and Weng Z (2005) Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics 21 Suppl 2():ii197-203 |
| Geijer C, et al. (2012) Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response. BMC Genomics 13(1):554 |
| 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 |
| Fondrat C and Kalogeropoulos A (1994) Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. Curr Genet 25(5):396-406 |
| 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 |
| Schlaepfer IR, et al. (1994) The sequence and potential regulatory elements of the HEM2 promoter of Saccharomyces cerevisiae. Yeast 10(2):227-9 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Morris RT, et al. (2010) Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics 26(2):168-74 |
| Ratnakumar S, et al. (2011) Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae. Mol Biosyst 7(1):139-49 |
| Smith JJ, et al. (2011) Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol 7():455 |