Identification of transcription factor binding sites using hybrid particle swarm optimization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3642 LNAI, Issue , 2005, Pages 438-445

  Zhou, Wengang ^a   Zhou, Chunguang ^a   Liu, Guixia ^a   Huang, Yanxin ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; GENES; IDENTIFICATION (CONTROL SYSTEMS); MUTAGENESIS; OPTIMIZATION;

COMBINATORIAL OPTIMIZATION; FACTOR BINDING SITES; SWARM OPTIMIZATION; TRANSCRIPTION FACTOR BINDING SITES (TFBS);

PROBLEM SOLVING;

EID: 33645957661     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11548706_46     Document Type: Conference Paper

References (10)

1. Collins, F., Green, E., Guttmacher, A., Guyer, M.: A Vision for the Future of Genomics Research. Nature, 422 (2003) 835-847
2. Lockhart, D., Winzeler, E.: Genomics, Gene Expression and DNA Arrays. Nature, 405 (2000) 827-836
3. Qin Z., McCue L., Thompson, W., Mayerhofer, L., Lawrence, C., Liu, J.: Identification of Co-regulated Genes Through Bayesian Clustering of Predicted Regulatory Binding Sites. Nature Biotechnology, 21 (2003) 435-439
4. Olman V., et al: Identification of Regulatory Binding Sites Using Minimum Spanning Trees. Proceedings of Pacific Symposium on Biocomputing (2003) 327-338
5. Cora, D., DiCunto, F., Provero, P., Silengo, L., Caselle, M.: Computational Identification of Transcription Factor Binding Sites by Functional Analysis of Sets of Genes Sharing Overrepresented Upstream Motifs. BMC Bioinformatics, 5 (2004) 57
6. Bailey, T., Elkan, C.: Fitting A Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers. Proceedings of International Conference on Intelligent Systems for Molecular Biology (1994) 28-36
7. Kennedy, J., Eberhart, R.C.: Particle Swarm Optimization. Proceedings of the IEEE International Conference on Neural Networks (1995) 1942-1948
8. Kel-Margoulis, O.V.: COMPEL: A Database on Composite Regulatory Elements Providing Combinatorial Transcriptional Regulation. Nucleic Acids Research, 28 (2003) 311-315
9. Fogel, G.B.: Discovery of Sequence Motifs Related to Coexpression of Genes Using Evolutionary Computation. Nucleic Acids Research, 32 (2004) 3826-3835
10. Rasmussen, T.K., Krink, T.: Improved Hidden Markov Model Training for Multiple Sequence Alignment by A Particle Swarm Optimization. Biosystems, 72 (2003) 5-17