| Vilela C and McCarthy JE (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region. Mol Microbiol 49(4):859-67 |
| 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 |
| 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 |
| Hood HM, et al. (2009) Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol 63:385-409 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35 |
| Lavoie H, et al. (2009) Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi. Curr Opin Microbiol 12(6):655-63 |
| Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45 |
| Selpi S, et al. (2009) Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC Bioinformatics 10():451 |
| 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 |
| Lipford JR, et al. (2005) A putative stimulatory role for activator turnover in gene expression. Nature 438(7064):113-6 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| 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 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |