A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

Bioinformatics

Volumn 26, Issue 12, 2010, Pages

  Chen, Xiaoyu ^a   Hoffman, Michael M ^b   Bilmes, Jeff A ^a   Hesselberth, Jay R ^b   Noble, William S ^a,b  

^a University of Washington   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE;

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BAYES THEOREM; BINDING SITE; CHEMISTRY; GENETICS; GENOME; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN FOOTPRINTING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION SITE;

ALGORITHMS; BAYES THEOREM; BINDING SITES; GENOME; MOLECULAR SEQUENCE DATA; PROTEIN FOOTPRINTING; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 77954199175     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq175     Document Type: Article

References (28)

1. Bilmes, J. and Bartels, C. (2005) Graphical model architectures for speech recognition. IEEE Signal Processing Magazine, 22, 89-100.
2. Bilmes, J. and Zweig, G. (2002) The Graphical Models Toolkit: An open source software system for speech and time-series processing. In Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, Orlando, USA, pp. 3916-3919.
3. Devlin, C. et al. (1991) RAP1 is required for BAS1/BAS2-and GCN4-dependent transcription of the yeast HIS4 gene. Mol. Cell Biol., 11, 3642-3651.
4. Dolan, J.W. et al. (1989) The yeast STE12 protein binds to the DNAsequence mediating pheromone induction. Proc. Natl Acad. Sci. USA, 86, 5703-5707.
5. Dorschner, M.O. et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. Nat. Methods, 1, 219-225.
6. Hesselberth, J.R. et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods, 6, 283-289.
7. Houseley, J. et al. (2008) A ncRNA modulates histone modification and mrna induction in the yeast GAL gene cluster. Mol. Cell, 32, 685-695.
8. Jarvis, E.E. et al. (1989) The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene. Genes Dev., 3, 936-945.
9. Johnson, D.S. et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
10. Keleher, C.A. et al. (1989) Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1. Mol. Cell Biol., 9, 5228-5230.
11. Klammer, A.A. et al. (2008) Modelling peptide fragmentation with dynamic Bayesian networks yields improved tandem mass spectrum identification. Bioinformatics, 24, i345-i356.
12. Lascaris, R.F. et al. (2000) Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res., 28, 1390-1396.
13. Lee, W. et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet., 39, 1235-1244.
14. MacIsaac, K.D. et al. (2006) An improved map of conserved regulatory sites for saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
15. Marion, R.M. et al. (2004) Sfp1 is a stress-and nutrient-sensitive regulator of ribosomal protein gene expression. Proc. Natl Acad. Sci. USA, 101, 14315-14322.
16. Mavrich, T.N. et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res., 18, 1073-1083.
17. Mead, J. et al. (2002) Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast. Mol. Cell Biol., 22, 4607-4621.
18. Perocchi, F. et al. (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res., 35, e128.
19. Ren, B. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
20. Reynolds, S.M. et al. (2008) Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol., 4, e1000213.
21. Robertson, G. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
22. Staden, R. (1994) Searching for motifs in nucleic acid sequences. Methods Mol. Biol., 25, 93-102.
23. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genome-wide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
24. Valouev, A. et al. (2008) Genome-wide analysis of transcription factor binding sites based on Chip-Seq data. Nat Methods, 5, 829-834.
25. Wu, C. (1980) The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature, 286, 854-860.
26. Yao, X.-Q. et al. (2008) A dynamic Bayesian network approach to protein secondary structure prediction. BMC Bioinformatics, 9, 49.
27. Yarragudi, A. et al. (2004) Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast saccharomyces cerevisiae. Mol. Cell Biol., 24, 9152-9164.
28. Zhu, C. et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res., 19, 556-566.