| Jones DL, et al. (2003) Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiol Genomics 16(1):107-18 |
| Tanay A, et al. (2004) A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res 14(5):829-34 |
| Xiao W and Rank GH (1990) Branched chain amino acid regulation of the ILV2 locus in Saccharomyces cerevisiae. Genome 33(4):596-603 |
| Wang D, et al. (1999) Yeast transcriptional regulator Leu3p. Self-masking, specificity of masking, and evidence for regulation by the intracellular level of Leu3p. J Biol Chem 274(27):19017-24 |
| Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7 |
| 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 |
| Didion T, et al. (1996) Amino acids induce expression of BAP2, a branched-chain amino acid permease gene in Saccharomyces cerevisiae. J Bacteriol 178(7):2025-9 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92 |
| Hahn S and Young ET (2011) Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators. Genetics 189(3):705-36 |
| Ulitsky I, et al. (2008) MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biol 9(1):R1 |
| Hinnebusch AG (1988) Mechanisms of gene regulation in the general control of amino acid biosynthesis in Saccharomyces cerevisiae. Microbiol Rev 52(2):248-73 |
| Alvers AL, et al. (2009) Autophagy and amino acid homeostasis are required for chronological longevity in Saccharomyces cerevisiae. Aging Cell 8(4):353-69 |
| Slavov N, et al. (2014) Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Rep 7(3):705-14 |
| 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 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| 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 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| 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 |
| Gunji W, et al. (2004) Global analysis of the regulatory network structure of gene expression in Saccharomyces cerevisiae. DNA Res 11(3):163-77 |
| Brisco PR and Kohlhaw GB (1990) Regulation of yeast LEU2. Total deletion of regulatory gene LEU3 unmasks GCN4-dependent basal level expression of LEU2. J Biol Chem 265(20):11667-75 |
| Xu B, et al. (2013) A structural-based strategy for recognition of transcription factor binding sites. PLoS One 8(1):e52460 |
| 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 |
| Sharon E, et al. (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.LID - 10.1038/nbt.2205 [doi] Nat Biotechnol () |
| Cao J, et al. (2012) Modeling gene regulation networks using ordinary differential equations. Methods Mol Biol 802():185-97 |
| Fendt SM, et al. (2010) Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol 6():432 |
| Harbison CT, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99-104 |
| 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 |
| Rossouw D and Bauer FF (2009) Comparing the transcriptomes of wine yeast strains: toward understanding the interaction between environment and transcriptome during fermentation. Appl Microbiol Biotechnol 84(5):937-54 |
| Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45 |
| 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 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| Boer VM, et al. (2005) Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res 5(10):885-97 |
| Aris JP, et al. (2012) Amino Acid Homeostasis and Chronological Longevity in Saccharomyces cerevisiae. Subcell Biochem 57():161-86 |
| Philpott CC, et al. (2012) Metabolic remodeling in iron-deficient fungi. Biochim Biophys Acta 1823(9):1509-20 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Sun W, et al. (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23(17):2290-7 |
| Roider H, et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23(2):134-41 |
| 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 |
| 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 |