UME6/YDR207C Literature Guide Help

Other names published for UME6: CAR80, NIM2, RIM16, YDR207C

UME6 - Computational analysis (24)

ReferenceOther Genes Addressed
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
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
Dikicioglu D, et al.  (2011) How yeast re-programmes its transcriptional profile in response to different nutrient impulses. BMC Syst Biol 5(1):148
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
Chen X, et al.  (2010) A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics 26(12):i334-42
Goh WS, et al.  (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6(1):e1000649
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
On T, et al.  (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89
Dai Z, et al.  (2009) Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications. BMC Genomics 10:304
Jothi R, et al.  (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Sardiu ME, et al.  (2009) Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One 4(10):e7310
Swamy KB, et al.  (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001
Lu CC, et al.  (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Wu WS and Li WH  (2008) Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics 9:439
Holloway DT, et al.  (2007) Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol 1(1):25-46
Steinfeld I, et al.  (2007) A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet 39(3):303-9
Guo X, et al.  (2006) Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22(4):392-9
Hart CE, et al.  (2006) Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2(12):e169
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
Yu T and Li KC  (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Luscombe NM, et al.  (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12
Caselle M, et al.  (2002) Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes. BMC Bioinformatics 3():7