| 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 |
| Yuan S and Li KC (2007) Context-dependent clustering for dynamic cellular state modeling of microarray gene expression. Bioinformatics 23(22):3039-47 |
| Leyfer D and Weng Z (2005) Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics 21 Suppl 2():ii197-203 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Deckert J and Struhl K (2001) Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol Cell Biol 21(8):2726-35 |
| 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 |
| 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 |
| Ward LD and Bussemaker HJ (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24(13):i165-71 |
| Titz B, et al. (2006) Transcriptional activators in yeast. Nucleic Acids Res 34(3):955-67 |
| 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 |
| 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 |
| 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 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |