The 28 papers which experimentally study the biological roles of both TFs of the PCTFP (Reb1-Mcm1)
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
Bai L, et al. (2011) Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter. Mol Cell 42(4):465-76
Chen AK, et al. (2009) Response of Saccharomyces cerevisiae to stress-free acidification. J Microbiol 47(1):1-8
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6
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
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
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
Shida K (2006) GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima. BMC Bioinformatics 7:486
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
Roider H, et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23(2):134-41
Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
Sharon E, et al. (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.LID - 10.1038/nbt.2205 [doi] Nat Biotechnol ()
Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Hu J, et al. (2010) Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast. Comput Biol Chem 34(2):106-14
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
Tanaka Y, et al. (2010) Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. Chromosoma 119(4):391-404
Wang X, et al. (2011) Nucleosomes and the accessibility problem. Trends Genet 27(12):487-92
Kamei Y, et al. (2015) Transcription factor genes essential for cell proliferation and replicative lifespan in budding yeast. Biochem Biophys Res Commun 463(3):351-6
Hesselberth JR, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283-9
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
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
Lin L, et al. (2012) Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4. Proc Natl Acad Sci U S A 109(6):1997-2002
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