| Sunnaker M, et al. (2013) Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key msn2 control mechanism. Sci Signal 6(277):ra41 | 
        
                
            | 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 | 
        
                
            | Carreto L, et al. (2011) Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains. BMC Genomics 12(1):201 | 
        
                
            | 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 | 
        
                
            | 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 | 
        
                
            | Teixeira MC, et al. (2007) Environmental genomics: mechanistic insights into toxicity of and resistance to the herbicide 2,4-D. Trends Biotechnol 25(8):363-70 | 
        
                
            | Albanese V, et al. (2006) Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells. Cell 124(1):75-88 | 
        
                
            | Elemento O, et al. (2007) A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types. Mol Cell 28(2):337-50 | 
        
                
            | 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 | 
        
                
            | Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 | 
        
                
            | Huebert DJ, et al. (2012) Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 32(9):1645-53 | 
        
                
            | Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 | 
        
                
            | Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74 | 
        
                
            | Middendorf M, et al. (2004) Predicting genetic regulatory response using classification. Bioinformatics 20 Suppl 1():i232-40 | 
        
                
            | 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 | 
        
                
            | Ho YH and Gasch AP (2015) Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 61(4):503-11 | 
        
                
            | Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 | 
        
                
            | 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 | 
        
                
            | Wu WS and Lai FJ (2015) Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. BMC Genomics 16 Suppl 12():S10 | 
        
                
            | Boorsma A, et al. (2004) Characterization of the transcriptional response to cell wall stress in Saccharomyces cerevisiae. Yeast 21(5):413-27 | 
        
                
            | Engelberg D, et al. (2014) Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 26(12):2865-78 | 
        
                
            | 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 | 
        
                
            | Chin SL, et al. (2012) Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J 279(6):1119-30 | 
        
                
            | Ye Y, et al. (2009) Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways. Biochem Biophys Res Commun 385(3):357-62 | 
        
                
            | Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 | 
        
                
            | Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 | 
        
                
            | de Virgilio C (2012) The essence of yeast quiescence. FEMS Microbiol Rev 36(2):306-39 | 
        
                
            | Conrad M, et al. (2014) Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):254-99 | 
        
                
            | Zanton SJ and Pugh BF (2006) Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 20(16):2250-65 | 
        
                
            | 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 |