| Tan K, et al. (2008) A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A 105(8):2934-9 |
| Yu L, et al. (2010) Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 88(1):219-29 |
| Salin H, et al. (2008) Structure and properties of transcriptional networks driving selenite stress response in yeasts. BMC Genomics 9:333 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Deppmann CD, et al. (2006) Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks. Mol Biol Evol 23(8):1480-92 |
| Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
| de Lucena RM, et al. (2012) Participation of CWI, HOG and Calcineurin pathways in the tolerance of Saccharomyces cerevisiae to low pH by inorganic acid. J Appl Microbiol 113(3):629-40 |
| Ma M and Liu ZL (2010) Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC G |
| Contador CA, et al. (2011) Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae. Biotechnol Prog 27(4):925-36 |
| Mazumder A, et al. (2013) Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 41(20):9310-24 |
| Lucau-Danila A, et al. (2005) Early expression of yeast genes affected by chemical stress. Mol Cell Biol 25(5):1860-8 |
| Nevitt T, et al. (2004) YAP4 gene expression is induced in response to several forms of stress in Saccharomyces cerevisiae. Yeast 21(16):1365-74 |
| 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 |
| 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 |
| 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 |
| Murray DB, et al. (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810(10):945-58 |
| Elsztein C, et al. (2011) The resistance of the yeast Saccharomyces cerevisiae to the biocide polyhexamethylene biguanide: involvement of cell wall integrity pathway and emerging role for YAP1. BMC Mol Biol 12(1):38 |
| Kuo D, et al. (2010) Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res 20(12):1672-8 |
| Manioudaki ME and Poirazi P (2013) Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet 4():110 |
| 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 |
| Agarwal AK, et al. (2008) Role of heme in the antifungal activity of the azaoxoaporphine alkaloid sampangine. Eukaryot Cell 7(2):387-400 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Rodrigues-Pousada C, et al. (2010) The Yap family and its role in stress response. Yeast 27(5):245-58 |
| 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 |
| Fernandes L, et al. (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17(12):6982-93 |
| Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9 |
| 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 |
| Khoury CM, et al. (2008) A TSC22-like motif defines a novel antiapoptotic protein family. FEMS Yeast Res 8(4):540-63 |
| 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 |
| Ouyang X, et al. (2011) Yap1 activation by H(2)O(2) or thiol-reactive chemicals elicits distinct adaptive gene responses. Free Radic Biol Med 50(1):1-13 |
| 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 |
| Kundaje A, et al. (2006) A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics 7 Suppl 1():S5 |