메뉴 건너뛰기




Volumn 36, Issue 2 PART 1, 2009, Pages 1039-1047

MOGAMOD: Multi-objective genetic algorithm for motif discovery

Author keywords

Motif discovery; Multi objective genetic algorithms; Transcription factors

Indexed keywords

DECISION MAKING; TRANSCRIPTION FACTORS;

EID: 56349123312     PISSN: 09574174     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.eswa.2007.11.008     Document Type: Article
Times cited : (67)

References (36)
  • 1
    • 0028685490 scopus 로고    scopus 로고
    • Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the second international conference ISMB, USA (pp. 28-36).
    • Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the second international conference ISMB, USA (pp. 28-36).
  • 2
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey T.L., and Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21 (1995) 51-80
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0034823882 scopus 로고    scopus 로고
    • Buhler, J., & Tompa, M. (2001). Finding motifs using random projections. In Proceedings RECOMB'01, Canada (pp. 69-76).
    • Buhler, J., & Tompa, M. (2001). Finding motifs using random projections. In Proceedings RECOMB'01, Canada (pp. 69-76).
  • 5
    • 32444449634 scopus 로고    scopus 로고
    • Che, D. (2005). MDGA: Motif discovery using a genetic algorithm. In Proc. GECCO'05, USA (pp. 447-452).
    • Che, D. (2005). MDGA: Motif discovery using a genetic algorithm. In Proc. GECCO'05, USA (pp. 447-452).
  • 6
    • 33847197149 scopus 로고    scopus 로고
    • Congdon, C. B. (2005). Preliminary results for GAMI: A genetic algorithms approach to motif inference. In Proc. CIBCB'05, USA (pp. 1-8).
    • Congdon, C. B. (2005). Preliminary results for GAMI: A genetic algorithms approach to motif inference. In Proc. CIBCB'05, USA (pp. 1-8).
  • 7
    • 0036530772 scopus 로고    scopus 로고
    • A fast and elitist multi-objective genetic algorithm: NSGA II
    • Deb K., et al. A fast and elitist multi-objective genetic algorithm: NSGA II. IEEE Transactions on Evolutionary Computation 6 (2002) 182-197
    • (2002) IEEE Transactions on Evolutionary Computation , vol.6 , pp. 182-197
    • Deb, K.1
  • 8
    • 33645748095 scopus 로고    scopus 로고
    • What are DNA sequence motifs?
    • D'heaseleer P. What are DNA sequence motifs?. National Biotechnology 24 (2006) 423-425
    • (2006) National Biotechnology , vol.24 , pp. 423-425
    • D'heaseleer, P.1
  • 9
    • 56349128414 scopus 로고
    • Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Irp regulon
    • Fraenkel Y., et al. Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Irp regulon. Computer Applications in the Biosciences (1995) 11
    • (1995) Computer Applications in the Biosciences , pp. 11
    • Fraenkel, Y.1
  • 10
    • 0034141782 scopus 로고    scopus 로고
    • Prediction of transcription regulatory sites in archaea by a comparative genomic approach
    • Gelfand M., et al. Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucleic Acids Research 28 (2000) 695-705
    • (2000) Nucleic Acids Research , vol.28 , pp. 695-705
    • Gelfand, M.1
  • 12
    • 0032136585 scopus 로고    scopus 로고
    • Tackling real-coded genetic algorithms: Operators and tools for behavioural analysis
    • Herrera F., et al. Tackling real-coded genetic algorithms: Operators and tools for behavioural analysis. Artificial Intelligence Review 12 (1998) 265-319
    • (1998) Artificial Intelligence Review , vol.12 , pp. 265-319
    • Herrera, F.1
  • 13
    • 56349150555 scopus 로고    scopus 로고
    • Hertz, G. Z., & Stormo, G. D. (1995). Identification of consensus patterns in unaligned DNA and protein sequences: A large-deviation statistical basis for penalizing gaps. In Proceedings of the international conference on bioinformatics and genome research (pp. 201-216).
    • Hertz, G. Z., & Stormo, G. D. (1995). Identification of consensus patterns in unaligned DNA and protein sequences: A large-deviation statistical basis for penalizing gaps. In Proceedings of the international conference on bioinformatics and genome research (pp. 201-216).
  • 14
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz G.Z., and Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 (1999) 563-577
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 16
    • 19544388921 scopus 로고    scopus 로고
    • Kaya, M., & Alhajj, R. (2004a). Integrating multi-objective genetic algorithms into clustering for fuzzy association rules mining. In: IEEE international conference on data mining (ICDM 2004), Brighton, UK, 1-4 November 2004.
    • Kaya, M., & Alhajj, R. (2004a). Integrating multi-objective genetic algorithms into clustering for fuzzy association rules mining. In: IEEE international conference on data mining (ICDM 2004), Brighton, UK, 1-4 November 2004.
  • 17
    • 16244389624 scopus 로고    scopus 로고
    • Kaya, M., & Alhajj, R. (2004b). Multi-objective genetic algorithm based approach for optimizing fuzzy sequential patterns. In 16th IEEE international conference on tools with artificial intelligence. Boca Raton: FL, USA.
    • Kaya, M., & Alhajj, R. (2004b). Multi-objective genetic algorithm based approach for optimizing fuzzy sequential patterns. In 16th IEEE international conference on tools with artificial intelligence. Boca Raton: FL, USA.
  • 18
    • 33244458239 scopus 로고    scopus 로고
    • Multi-objective genetic algorithm based approaches for mining optimized fuzzy association rules
    • Kaya M. Multi-objective genetic algorithm based approaches for mining optimized fuzzy association rules. Soft Computing Journal 10 7 (2006) 578-586
    • (2006) Soft Computing Journal , vol.10 , Issue.7 , pp. 578-586
    • Kaya, M.1
  • 19
    • 0032654634 scopus 로고    scopus 로고
    • Li, M., Ma, B., & Wang, L. (1999). Finding similar regions in many strings. In Proceedings STOC, USA (pp. 473-482).
    • Li, M., Ma, B., & Wang, L. (1999). Finding similar regions in many strings. In Proceedings STOC, USA (pp. 473-482).
  • 20
    • 4544358562 scopus 로고    scopus 로고
    • Liu, F. M. (2004). FMGA: Finding motifs by genetic algorithm. In Proceedings BIBE'04, Taiwan (pp. 459-466).
    • Liu, F. M. (2004). FMGA: Finding motifs by genetic algorithm. In Proceedings BIBE'04, Taiwan (pp. 459-466).
  • 21
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame C., and Higgins D.G. SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Research 24 (1996) 1515-1524
    • (1996) Nucleic Acids Research , vol.24 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.G.2
  • 22
    • 33750275579 scopus 로고    scopus 로고
    • Paul, T. K., & Iba, H. (2006). Identification of weak motifs in multiple biological sequences using genetic algorithm. In Proceedings GECCO'06, USA (pp. 271-278).
    • Paul, T. K., & Iba, H. (2006). Identification of weak motifs in multiple biological sequences using genetic algorithm. In Proceedings GECCO'06, USA (pp. 271-278).
  • 23
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Pavesi G., et al. Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research 32 (2004) W199-W203
    • (2004) Nucleic Acids Research , vol.32
    • Pavesi, G.1
  • 24
    • 0026729501 scopus 로고
    • Wordup: An efficient algorithm for discovering statistically significant patterns in DNA sequences
    • Pesole G., et al. Wordup: An efficient algorithm for discovering statistically significant patterns in DNA sequences. Journal of Nucleic Acids Research 20 (1992) 2871-2875
    • (1992) Journal of Nucleic Acids Research , vol.20 , pp. 2871-2875
    • Pesole, G.1
  • 25
    • 0034565285 scopus 로고    scopus 로고
    • Pevzner, P., & Sze, S. H. (2000). Combinatorial approaches to finding subtle in DNA sequences. In Proceedings ISMB'00 (pp. 269-278).
    • Pevzner, P., & Sze, S. H. (2000). Combinatorial approaches to finding subtle in DNA sequences. In Proceedings ISMB'00 (pp. 269-278).
  • 26
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • Roth F.P., et al. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. National Biotechnology 16 (1998) 939-945
    • (1998) National Biotechnology , vol.16 , pp. 939-945
    • Roth, F.P.1
  • 27
    • 0042905768 scopus 로고    scopus 로고
    • YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha S., and Tompa M. YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research 31 (2003) 3586-3588
    • (2003) Nucleic Acids Research , vol.31 , pp. 3586-3588
    • Sinha, S.1    Tompa, M.2
  • 28
    • 84901431286 scopus 로고    scopus 로고
    • Stine, M. (2003). Motif discovery in upstream sequences of coordinately expressed genes. CEC'03, USA (pp. 1596-1603).
    • Stine, M. (2003). Motif discovery in upstream sequences of coordinately expressed genes. CEC'03, USA (pp. 1596-1603).
  • 29
    • 0032964297 scopus 로고    scopus 로고
    • Blast2 sequences, a new tool for comparing protein and nucleotide sequences
    • Tatusova T.A., and Madden T.L. Blast2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiology Letters 2 (1999) 247-250
    • (1999) FEMS Microbiology Letters , vol.2 , pp. 247-250
    • Tatusova, T.A.1    Madden, T.L.2
  • 30
    • 0036108622 scopus 로고    scopus 로고
    • A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    • Thijs G., et al. A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. Journal of Computational Biology 9 (2002) 447-464
    • (2002) Journal of Computational Biology , vol.9 , pp. 447-464
    • Thijs, G.1
  • 31
    • 0043123063 scopus 로고    scopus 로고
    • Gibbs recursive sampler: Finding transcription factor binding sites
    • Thompson W., et al. Gibbs recursive sampler: Finding transcription factor binding sites. Journal of Nucleic Acids Research 31 (2003) 3580-3585
    • (2003) Journal of Nucleic Acids Research , vol.31 , pp. 3580-3585
    • Thompson, W.1
  • 32
    • 0033289316 scopus 로고    scopus 로고
    • Tompa, M. (1999). An exact method for finding short motifs in sequences with application to the ribosome binding site problem. In Proceedings of the international conference on ISMB, Germany (pp. 262-271).
    • Tompa, M. (1999). An exact method for finding short motifs in sequences with application to the ribosome binding site problem. In Proceedings of the international conference on ISMB, Germany (pp. 262-271).
  • 33
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa M., et al. Assessing computational tools for the discovery of transcription factor binding sites. National Biotechnology 23 (2005) 137-144
    • (2005) National Biotechnology , vol.23 , pp. 137-144
    • Tompa, M.1
  • 34
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • Van Helden J., et al. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 281 (1998) 827-842
    • (1998) Journal of Molecular Biology , vol.281 , pp. 827-842
    • Van Helden, J.1
  • 35
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender E., et al. TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Research 24 (1996) 238-241
    • (1996) Nucleic Acids Research , vol.24 , pp. 238-241
    • Wingender, E.1
  • 36
    • 0034199979 scopus 로고    scopus 로고
    • Comparison of multiobjective evolutionary algorithms: Empirical results
    • Zitzler E., et al. Comparison of multiobjective evolutionary algorithms: Empirical results. Evolutionary Computation 2 (2000) 173-195
    • (2000) Evolutionary Computation , vol.2 , pp. 173-195
    • Zitzler, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.