Regulatory Element Detection using a Probabilistic Segmentation Model

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, ISMB 2000

Volumn , Issue , 2000, Pages 67-74

  Bussemaker, Harmen J ^a   Li, Hao ^b   Siggia, Eric D ^b,c  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b ROCKEFELLER UNIVERSITY   (United States)

^c Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; NUCLEIC ACIDS;

CONTROL REGION; DATA SET; ELEMENTS DETECTION; EXPRESSION DATA; MRNA EXPRESSION; PROBABILISTICS; REFERENCE DATA; REGULATORY ELEMENTS; REGULATORY REGIONS; SEGMENTATION MODELS;

TRANSCRIPTION;

MESSENGER RNA;

ALGORITHM; ANIMAL; ARTICLE; GENETICS; GENOME; HUMAN; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; GENOME; HUMANS; RNA, MESSENGER; SEQUENCE ANALYSIS;

EID: 0034565040     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (12)

1. Bailey, T., and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings ISMB'94 28-36.
2. Brazma, A.; Johnassen, I.; Vilo, J.; and Ukkonen, E. 1998. Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8:1202-1215.
3. Bussemaker, H. J.; Li, H.; and Siggia, E. D. 2000. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Submitted.
4. Chu, S.; DeRisi, J.; Eisen, M.; Mulholland, J.; et al. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705.
5. Eisen, M. B.; Spellman, P. T.; Brown, P. O.; and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:14863-14868.
6. Lawrence, C. E.; Altshul, S. F.; Boguski, M. S.; Liu, J. S.; et al. 1993. Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science 262:208-214.
7. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; and Flannery, B. P. 1992. Numerical Recipes in C. Cambridge University Press.
8. Rigoutsos, I., and Floratos, A. 1998. Combinatorial pattern discovery in biological sequences: The TEREISIAS algorithm. Bioinformatics 14:55-67.
9. Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; et al. 1998. Comprehensive identification of cell cycleregulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9:3273-3297.
10. Stormo, G. D., and Hartzell, G. W. 1989. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 86:1183-1187.
11. van Helden, J.; André, B.; and Collado-Vides, J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281:827-842.
12. Zhu, J., and Zhang, M. Q. 1999. SCPD: A promoter database of yeast saccharomyces cerevisiae. Bioinformatics 15:607-611.