| Yu L, et al. (2010) Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 88(1):219-29 |
| Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
| Moye-Rowley WS, et al. (1989) Yeast YAP1 encodes a novel form of the jun family of transcriptional activator proteins. Genes Dev 3(3):283-92 |
| Selpi S, et al. (2009) Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC Bioinformatics 10():451 |
| 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 |
| Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74 |
| Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358 |
| Wu A, et al. (1993) Yeast bZip proteins mediate pleiotropic drug and metal resistance. J Biol Chem 268(25):18850-8 |
| Kandror O, et al. (2004) Yeast adapt to near-freezing temperatures by STRE/Msn2,4-dependent induction of trehalose synthesis and certain molecular chaperones. Mol Cell 13(6):771-81 |
| Nomura W, et al. (2008) Role of Gcn4 for adaptation to methylglyoxal in Saccharomyces cerevisiae: methylglyoxal attenuates protein synthesis through phosphorylation of eIF2alpha. Biochem Biophys Res Commun 376(4):738-42 |
| Vilela C, et al. (1999) Post-termination ribosome interactions with the 5'UTR modulate yeast mRNA stability. EMBO J 18(11):3139-52 |
| Kruegel U, et al. (2011) Elevated Proteasome Capacity Extends Replicative Lifespan in Saccharomyces cerevisiae. PLoS Genet 7(9):e1002253 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Teixeira MC, et al. (2011) Yeast response and tolerance to polyamine toxicity involving the drug: H+ antiporter Qdr3 and the transcription factors Yap1 and Gcn4. Microbiology 157(Pt 4):945-56 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| 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 |
| 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 |
| Taylor MP, et al. (2012) Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations. Biotechnol J 7(9):1169-81 |
| Mohammadi S, et al. (2013) Inferring the Effective TOR-Dependent Network: A Computational Study in Yeast. BMC Syst Biol 7(1):84 |
| Mager WH and De Kruijff AJ (1995) Stress-induced transcriptional activation. Microbiol Rev 59(3):506-31 |
| Vincent AC and Struhl K (1992) ACR1, a yeast ATF/CREB repressor. Mol Cell Biol 12(12):5394-405 |
| Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94 |
| 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 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Murray DB, et al. (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810(10):945-58 |
| Zeng T and Li J (2010) Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways. Nucleic Acids Res 38(1):e1 |
| Ruiz-Echevarria MJ and Peltz SW (2000) The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames. Cell 101(7):741-51 |
| Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
| Coleman ST, et al. (1997) Saccharomyces cerevisiae basic region-leucine zipper protein regulatory networks converge at the ATR1 structural gene. J Biol Chem 272(37):23224-30 |
| Molin M, et al. (2011) Life Span Extension and H(2)O(2) Resistance Elicited by Caloric Restriction Require the Peroxiredoxin Tsa1 in Saccharomyces cerevisiae. Mol Cell 43(5):823-33 |
| Cvijovic M, et al. (2007) Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation. BMC Bioinformatics 8:295 |
| 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 |
| Middendorf M, et al. (2004) Predicting genetic regulatory response using classification. Bioinformatics 20 Suppl 1():i232-40 |
| 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 |
| Bajwa PK, et al. (2013) Transcriptional profiling of Saccharomyces cerevisiae T2 cells upon exposure to hardwood spent sulphite liquor: comparison to acetic acid, furfural and hydroxymethylfurfural. Antonie Van Leeuwenhoek 103(6):1281-95 |
| Gordan R, et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 19(11):2090-100 |
| 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 |
| Uluisik I, et al. (2011) Boron stress activates the general amino acid control mechanism and inhibits protein synthesis. PLoS One 6(11):e27772 |
| Wawrzycka D, et al. (2010) Vmr 1p is a novel vacuolar multidrug resistance ABC transporter in Saccharomyces cerevisiae. FEMS Yeast Res 10(7):828-38 |
| Feng X and Zhao H (2013) Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis. Biotechnol Biofuels 6(1):96 |
| Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70 |
| Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45 |
| 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 |
| 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 |
| Bruckner S and Mosch HU (2012) Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev 36(1):25-58 |
| Ye C, et al. (2009) Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol 5(3):e1000311 |
| Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9 |
| Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |
| 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 |
| Harshman KD, et al. (1988) Transcriptional activation by the SV40 AP-1 recognition element in yeast is mediated by a factor similar to AP-1 that is distinct from GCN4. Cell 53(2):321-30 |
| 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 |
| Fry RC, et al. (2005) Genome-wide responses to DNA-damaging agents. Annu Rev Microbiol 59():357-77 |
| Stotz A, et al. (1993) Regulation of the ADE2 gene from Saccharomyces cerevisiae. Curr Genet 24(6):472-80 |
| Wout PK, et al. (2009) Saccharomyces cerevisiae Rbg1 protein and its binding partner Gir2 interact on Polyribosomes with Gcn1. Eukaryot Cell 8(7):1061-71 |
| 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 |