| McIsaac RS, et al. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell 23(15):2993-3007 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Dormer UH, et al. (2000) Cadmium-inducible expression of the yeast GSH1 gene requires a functional sulfur-amino acid regulatory network. J Biol Chem 275(42):32611-6 |
| Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
| Gertz J and Cohen BA (2009) Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol 5:244 |
| Cormier L, et al. (2010) Transcriptional plasticity through differential assembly of a multiprotein activation complex. Nucleic Acids Res 38(15):4998-5014 |
| Zeigler RD and Cohen BA (2014) Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. Nucleic Acids Res 42(4):2224-34 |
| 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 |
| Ouni I, et al. (2010) A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors. Mol Cell 40(6):954-64 |
| 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 |
| Moxley JF, et al. (2009) Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A 106(16):6477-82 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| 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 |
| Siggers T, et al. (2011) Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol 7():555 |
| Carrillo E, et al. (2012) Characterizing the roles of Met31 and Met32 in coordinating Met4-activated transcription in the absence of Met30. Mol Biol Cell 23(10):1928-42 |
| Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35 |
| Ouni I, et al. (2011) Ubiquitin and transcription: The SCF/Met4 pathway, a (protein-) complex issue. Transcription 2(3):135-139 |
| Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Carreto L, et al. (2011) Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. BMC Genomics 12(1):201 |
| Lee TA, et al. (2010) Dissection of combinatorial control by the met4 transcriptional complex. Mol Biol Cell 21(3):456-69 |
| 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 |
| Chiang DY, et al. (2006) Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 7():16 |
| Thomas D and Surdin-Kerjan Y (1997) Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61(4):503-32 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Rouillon A, et al. (2000) Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCF(Met30 )complex. EMBO J 19(2):282-94 |
| 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 |
| Linder T (2012) Genomics of alternative sulfur utilization in ascomycetous yeasts. Microbiology 158(Pt 10):2585-97 |
| 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 |
| Ljungdahl PO and Daignan-Fornier B (2012) Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae. Genetics 190(3):885-929 |
| Su NY, et al. (2008) A Dominant Suppressor Mutation of the met30 Cell Cycle Defect Suggests Regulation of the Saccharomyces cerevisiae Met4-Cbf1 Transcription Complex by Met32. J Biol Chem 283(17):11615-24 |
| Kasavi C, et al. (2014) A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. BMC Syst Biol 8(1):90 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Hebert A, et al. (2011) Biodiversity in sulfur metabolism in hemiascomycetous yeasts. FEMS Yeast Res 11(4):366-78 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Blaiseau PL and Thomas D (1998) Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J 17(21):6327-36 |
| 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 |
| Petti AA, et al. (2012) Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell 23(15):3008-24 |