PHO4/YFR034C Literature Guide Help

Other names published for PHO4: phoD, YFR034C

PHO4 - Computational analysis (25)

ReferenceOther Genes Addressed
Achcar F, et al.  (2011) A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. BMC Syst Biol 5(1):51
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
Babbitt GA  (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Joshi A, et al.  (2010) Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol 11(3):R32
Morris RT, et al.  (2010) Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics 26(2):168-74
Emmert-Streib F and Dehmer M  (2009) Information processing in the transcriptional regulatory network of yeast: fnctional robustness. BMC Syst Biol 3:35
Jothi R, et al.  (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Nguyen Ba AN, et al.  (2009) NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics 10:202
Raveh-Sadka T, et al.  (2009) Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19(8):1480-96
Wang Y, et al.  (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res 37(18):5943-58
Lu CC, et al.  (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Chen G, et al.  (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4
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
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
Galbraith SJ, et al.  (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94
Wu WS, et al.  (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421
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
Gonze D, et al.  (2005) Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics 21(17):3490-500
Reneker J and Shyu CR  (2005) Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. BMC Bioinformatics 6():111
Siddharthan R, et al.  (2005) PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 1(7):e67
Luscombe NM, et al.  (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
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
Wang W, et al.  (2002) A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae. Proc Natl Acad Sci U S A 99(26):16893-8
Birnbaum K, et al.  (2001) cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Res 11(9):1567-73
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