| 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 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Martinez JL, et al. (2014) Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology. FEMS Yeast Res 14(4): |
| Rao AR and Pellegrini M (2011) Regulation of the yeast metabolic cycle by transcription factors with periodic activities. BMC Syst Biol 5(1):160 |
| 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 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| Koren A, et al. (2002) Control of meiotic recombination initiation: a role for the environment? Curr Genet 42(3):129-39 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Tsoi BM, et al. (2009) Essential Role of One-carbon Metabolism and Gcn4p and Bas1p Transcriptional Regulators during Adaptation to Anaerobic Growth of Saccharomyces cerevisiae. J Biol Chem 284(17):11205-15 |
| Gunji W, et al. (2004) Global analysis of the regulatory network structure of gene expression in Saccharomyces cerevisiae. DNA Res 11(3):163-77 |
| Arndt KT, et al. (1987) Multiple global regulators control HIS4 transcription in yeast. Science 237(4817):874-80 |
| 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 |
| Springer C, et al. (1997) Regulation of the yeast HIS7 gene by the global transcription factor Abf1p. Mol Gen Genet 256(2):136-46 |
| 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 |
| Pellman D, et al. (1990) TATA-dependent and TATA-independent transcription at the HIS4 gene of yeast. Nature 348(6296):82-5 |
| 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 |
| Han SJ, et al. (1999) Activator-specific requirement of yeast mediator proteins for RNA polymerase II transcriptional activation. Mol Cell Biol 19(2):979-88 |
| Valerius O, et al. (2003) Nucleosome position-dependent and -independent activation of HIS7 epression in Saccharomyces cerevisiae by different transcriptional activators. Eukaryot Cell 2(5):876-85 |
| 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 |
| Birnbaum K, et al. (2001) cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Res 11(9):1567-73 |
| Fendt SM, et al. (2010) Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol 6():432 |
| Tice-Baldwin K, et al. (1989) BAS1 has a Myb motif and activates HIS4 transcription only in combination with BAS2. Science 246(4932):931-5 |
| Arndt KT, et al. (1989) A suppressor of a HIS4 transcriptional defect encodes a protein with homology to the catalytic subunit of protein phosphatases. Cell 56(4):527-37 |
| 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 |
| Ljungdahl PO and Daignan-Fornier B (2012) Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae. Genetics 190(3):885-929 |
| Devlin C, et al. (1991) RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol 11(7):3642-51 |
| Subramanian M, et al. (2005) Transcriptional regulation of the one-carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p. Mol Microbiol 57(1):53-69 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Lamas-Maceiras M, et al. (1999) Kluyveromyces lactis HIS4 transcriptional regulation: similarities and differences to Saccharomyces cerevisiae HIS4 gene. FEBS Lett 458(1):72-6 |
| 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 |
| Springer C, et al. (1996) Amino acid and adenine cross-pathway regulation act through the same 5'-TGACTC-3' motif in the yeast HIS7 promoter. J Biol Chem 271(47):29637-43 |
| Dudley AM, et al. (1999) Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae. Genetics 151(4):1365-78 |
| Fordyce PM, et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28(9):970-5 |
| Stotz A, et al. (1993) Regulation of the ADE2 gene from Saccharomyces cerevisiae. Curr Genet 24(6):472-80 |
| Joo YJ, et al. (2009) Cooperative regulation of ADE3 transcription by Gcn4p and Bas1p in Saccharomyces cerevisiae. Eukaryot Cell 8(8):1268-77 |
| ter Schure EG, et al. (2000) The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. FEMS Microbiol Rev 24(1):67-83 |