| Ozonov EA and van Nimwegen E (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput Biol 9(8):e1003181 | 
        
                
            | Hart CE, et al. (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169 | 
        
                
            | Chen X, et al. (2010) A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics 26(12):i334-42 | 
        
                
            | Ho SW, et al. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A 103(26):9940-5 | 
        
                
            | Choi JK and Kim YJ (2008) Epigenetic regulation and the variability of gene expression. Nat Genet 40(2):141-7 | 
        
                
            | 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 | 
        
                
            | Park HD, et al. (1999) Synergistic operation of the CAR2 (Ornithine transaminase) promoter elements in Saccharomyces cerevisiae. J Bacteriol 181(22):7052-64 | 
        
                
            | 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 | 
        
                
            | On T, et al. (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89 | 
        
                
            | 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 | 
        
                
            | Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87 | 
        
                
            | Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001 | 
        
                
            | Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 | 
        
                
            | Kratzer S and Schuller HJ (1997) Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6. Mol Microbiol 26(4):631-41 | 
        
                
            | Henikoff JG, et al. (2011) Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A 108(45):18318-23 | 
        
                
            | Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421 | 
        
                
            | 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 | 
        
                
            | Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414 | 
        
                
            | Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 | 
        
                
            | Schlecht U and Primig M (2003) Mining meiosis and gametogenesis with DNA microarrays. Reproduction 125(4):447-56 | 
        
                
            | Einerhand AW, et al. (1995) The upstream region of the FOX3 gene encoding peroxisomal 3-oxoacyl-coenzyme A thiolase in Saccharomyces cerevisiae contains ABF1- and replication protein A-binding sites that participate in its regulation by glucose repression | 
        
                
            | Holloway DT, et al. (2007) Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol 1(1):25-46 | 
        
                
            | Guo X, et al. (2006) Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22(4):392-9 | 
        
                
            | Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 | 
        
                
            | 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 | 
        
                
            | Shimizu M, et al. (2003) Yeast Ume6p repressor permits activator binding but restricts TBP binding at the HOP1 promoter. Nucleic Acids Res 31(12):3033-7 | 
        
                
            | Tevzadze GG, et al. (2007) Genetic evidence for a SPO1-dependent signaling pathway controlling meiotic progression in yeast. Genetics 175(3):1213-27 | 
        
                
            | Dubois E and Messenguy F (1997) Integration of the multiple controls regulating the expression of the arginase gene CAR1 of Saccharomyces cerevisiae in response to differentnitrogen signals: role of Gln3p, ArgRp-Mcm1p, and Ume6p. Mol Gen Genet 253(5):568- | 
        
                
            | Tabancay AP Jr and Forsburg SL (2006) Eukaryotic DNA replication in a chromatin context. Curr Top Dev Biol 76():129-84 | 
        
                
            | 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 | 
        
                
            | Woo DK, et al. (2009) Multiple pathways of mitochondrial-nuclear communication in yeast: Intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation. Biochim Biophys Acta 1789(2):135-45 |