| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Biddick R and Young ET (2009) The disorderly study of ordered recruitment. Yeast 26(4):205-20 |
| Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87 |
| Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
| Gunji W, et al. (2004) Global analysis of the regulatory network structure of gene expression in Saccharomyces cerevisiae. DNA Res 11(3):163-77 |
| 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 |
| Yang Z, et al. (2010) Positive or negative roles of different cyclin-dependent kinase Pho85-cyclin complexes orchestrate induction of autophagy in Saccharomyces cerevisiae. Mol Cell 38(2):250-64 |
| 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 |
| O'Connell KF, et al. (1995) Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription. Mol Cell Biol 15(4):1879-88 |
| Nishizawa M, et al. (2008) Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast. PLoS Biol 6(12):e326 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Raveh-Sadka T, et al. (2009) Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19(8):1480-96 |
| Harashima S, et al. (1995) Mutations causing high basal level transcription that is independent of transcriptional activators but dependent on chromosomal position in Saccharomyces cerevisiae. Mol Gen Genet 247(6):716-25 |
| Kumar L, et al. (2010) Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. BMC Genomics 11():208 |
| 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 |
| 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 |
| Conlon EM, et al. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A 100(6):3339-44 |
| Sambuk EV, et al. (2005) [The lack of cyclin-dependent phosphoprotein kinase Pho85p leads to defects in mitochondrial nucleoid transmission in yeast Saccharomyces cerevisiae] Tsitologiia 47(10):917-24 |
| Raveh-Sadka T, et al. (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast.LID - 10.1038/ng.2305 [doi] Nat Genet () |
| 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 |
| 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 |
| Wang Y, et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58 |
| Nguyen Ba AN, et al. (2009) NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics 10:202 |
| 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 |
| Conrad M, et al. (2014) Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):254-99 |
| 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 |
| 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 |