메뉴 건너뛰기




Volumn 94, Issue , 2008, Pages 113-147

Swarm intelligence algorithms in bioinformatics

Author keywords

[No Author keywords available]

Indexed keywords


EID: 38049078025     PISSN: 1860949X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-76803-6_4     Document Type: Article
Times cited : (88)

References (100)
  • 11
    • 0003401932 scopus 로고
    • Ph.D. dissertation in Italian, Dipartimento di Elettronica, Politecnico di Milano, Milano, Italy
    • Dorigo M (1992) Optimization, learning, and natural algorithms, Ph.D. dissertation (in Italian), Dipartimento di Elettronica, Politecnico di Milano, Milano, Italy.
    • (1992) Optimization, learning, and natural algorithms
    • Dorigo, M.1
  • 12
    • 84901418243 scopus 로고    scopus 로고
    • Ant colony optimization: A new meta-heuristic
    • PJ Angeline, Z Michalewicz, M Schoenauer, X Yao, and A Zalzala, eds, IEEE Press
    • Dorigo M, Di Caro G and Gambardella L (1999) Ant colony optimization: A new meta-heuristic. In PJ Angeline, Z Michalewicz, M Schoenauer, X Yao, and A Zalzala, (eds), Proceedings of the Congress on Evolutionary Computation, IEEE Press, Vol. 2, pp. 1470-1477.
    • (1999) Proceedings of the Congress on Evolutionary Computation , vol.2 , pp. 1470-1477
    • Dorigo, M.1    Di Caro, G.2    Gambardella, L.3
  • 13
    • 0004238344 scopus 로고
    • Oxford University Press, New York, NY
    • Lewin B (1995) Genes VII. Oxford University Press, New York, NY.
    • (1995) Genes VII
    • Lewin, B.1
  • 16
    • 38049064568 scopus 로고    scopus 로고
    • http://en.wikipedia.org/wiki/DNA_microarray
  • 19
    • 0001287743 scopus 로고
    • The sensory basis of fish schools: Relative role of lateral line and vision
    • Partridge BL, Pitcher TJ (1980) The sensory basis of fish schools: relative role of lateral line and vision. Journal of Comparative Physiology, 135, pp. 315-325.
    • (1980) Journal of Comparative Physiology , vol.135 , pp. 315-325
    • Partridge, B.L.1    Pitcher, T.J.2
  • 20
    • 0011067237 scopus 로고
    • The structure and function of fish schools
    • Partridge BL (1982) The structure and function of fish schools. Science American, 245, pp. 90-99.
    • (1982) Science American , vol.245 , pp. 90-99
    • Partridge, B.L.1
  • 21
    • 0001555597 scopus 로고
    • The three-dimensional structure of airborne bird flocks
    • Major PF, Dill LM (1978) The three-dimensional structure of airborne bird flocks. Behavioral Ecology and Sociobiology, 4, pp. 111-122.
    • (1978) Behavioral Ecology and Sociobiology , vol.4 , pp. 111-122
    • Major, P.F.1    Dill, L.M.2
  • 24
    • 0000239536 scopus 로고
    • Swarms, phase transitions, and collective intelligence
    • Langton CG Ed, Addison Wesley, Reading, MA
    • Milonas MM (1994) Swarms, phase transitions, and collective intelligence, In Langton CG Ed., Artificial Life III, Addison Wesley, Reading, MA.
    • (1994) Artificial Life III
    • Milonas, M.M.1
  • 29
    • 0031122887 scopus 로고    scopus 로고
    • Ant colony system: A cooperative learning approach to the traveling salesman problem
    • Dorigo M and Gambardella LM (1997) Ant colony system: A cooperative learning approach to the traveling salesman problem, IEEE Trans. Evol. Comput., vol. 1, pp. 53-66.
    • (1997) IEEE Trans. Evol. Comput , vol.1 , pp. 53-66
    • Dorigo, M.1    Gambardella, L.M.2
  • 30
    • 34250300573 scopus 로고    scopus 로고
    • Application de I'ordre par fluctuations? la descriptio de certaines? tapes de la construction dun id chez les termites
    • Deneubourg JL (1997) Application de I'ordre par fluctuations? la descriptio de certaines? tapes de la construction dun id chez les termites, Insect Sociaux, vol. 24, pp. 117-130.
    • (1997) Insect Sociaux , vol.24 , pp. 117-130
    • Deneubourg, J.L.1
  • 31
    • 0030082551 scopus 로고    scopus 로고
    • Dorigo M, Maniezzo V and Colorni A (1996) The ant system: Optimization by a colony of cooperating agents, IEEE Trans. Syst. Man Cybern. B, 26.
    • Dorigo M, Maniezzo V and Colorni A (1996) The ant system: Optimization by a colony of cooperating agents, IEEE Trans. Syst. Man Cybern. B, vol. 26.
  • 32
    • 84899047533 scopus 로고    scopus 로고
    • Small Worlds and Mega-Minds: Effects of Neighborhood Topology on Particle Swarm Performance
    • IEEE Press, pp
    • Kennedy J (1999) Small Worlds and Mega-Minds: Effects of Neighborhood Topology on Particle Swarm Performance, Proceedings of the 1999 Congress of Evolutionary Computation, vol. 3, IEEE Press, pp. 1931-1938.
    • (1999) Proceedings of the 1999 Congress of Evolutionary Computation , vol.3 , pp. 1931-1938
    • Kennedy, J.1
  • 34
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of small-world networks
    • Watts DJ and Strogatz SH (1998) Collective dynamics of small-world networks. Nature, 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 36
    • 0042527883 scopus 로고    scopus 로고
    • On the properties of small-world network models
    • Barrat A and Weight M (2000) On the properties of small-world network models. The European Physical Journal, 13, pp. 547-560.
    • (2000) The European Physical Journal , vol.13 , pp. 547-560
    • Barrat, A.1    Weight, M.2
  • 37
    • 0034186340 scopus 로고    scopus 로고
    • Epidemics and percolation in small-world networks
    • Moore C and Newman MEJ (2000) Epidemics and percolation in small-world networks. Physics. Review. E 61, 5678-5682.
    • (2000) Physics. Review. E , vol.61 , pp. 5678-5682
    • Moore, C.1    Newman, M.E.J.2
  • 38
    • 0035686398 scopus 로고    scopus 로고
    • Trapping of random walks on small-world networks
    • Jasch F and Blumen A (2001) Trapping of random walks on small-world networks. Physical Review E 64, 066104.
    • (2001) Physical Review E , vol.64 , pp. 066104
    • Jasch, F.1    Blumen, A.2
  • 40
    • 4344714817 scopus 로고    scopus 로고
    • A comparative study of differential evolution, particle swarm optimization, and evolutionary algorithms on numerical benchmark problems
    • IEEE Press, pp
    • Vesterstrom J and Thomsen R (2004) A comparative study of differential evolution, particle swarm optimization, and evolutionary algorithms on numerical benchmark problems, In Proceedings of the IEEE Congress on Evolutionary Computation (CEC 04), IEEE Press, pp. 1980-1987.
    • (2004) Proceedings of the IEEE Congress on Evolutionary Computation (CEC 04) , pp. 1980-1987
    • Vesterstrom, J.1    Thomsen, R.2
  • 44
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray
    • data
    • Quackenbush J (2001) Computational analysis of microarray data, National Review of Genetics, vol. 2, pp. 418-427.
    • (2001) National Review of Genetics , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 45
    • 38049044477 scopus 로고    scopus 로고
    • Special Issue on Bioinformatics, IEEE Computer, 35, July 2002.
    • Special Issue on Bioinformatics, IEEE Computer, vol. 35, July 2002.
  • 48
    • 0033536012 scopus 로고    scopus 로고
    • Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays
    • Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D and Levine AJ (1999) Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays, Proc. Natl. Acad. Sci. USA, Cell Biology, Vol. 96, pp. 6745-6750.
    • (1999) Proc. Natl. Acad. Sci. USA, Cell Biology , vol.96 , pp. 6745-6750
    • Alon, U.1    Barkai, N.2    Notterman, D.A.3    Gish, K.4    Ybarra, S.5    Mack, D.6    Levine, A.J.7
  • 51
    • 0032441150 scopus 로고    scopus 로고
    • Cluster Analysis and Display of Genome-wide expression patterns
    • Spellman EM, Brown PL, Brown D (1998) Cluster Analysis and Display of Genome-wide expression patterns, Proc. Natl. Acad. Sci. USA 95: 14863-14868.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 14863-14868
    • Spellman, E.M.1    Brown, P.L.2    Brown, D.3
  • 52
    • 0034800371 scopus 로고    scopus 로고
    • Principal Component Analysis for Clustering Gene Expression Data
    • Yeung KY, Ruzzo WL (2001) Principal Component Analysis for Clustering Gene Expression Data, Bioinformatics, 17, pp. 763-774.
    • (2001) Bioinformatics , vol.17 , pp. 763-774
    • Yeung, K.Y.1    Ruzzo, W.L.2
  • 53
    • 38049093964 scopus 로고    scopus 로고
    • Raychaudhuri S, Stuart JM and Altman RB (2000) Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series, Pacific Symposium on Biocomputing 2000, Honolulu, Hawaii, pp. 452-463.
    • Raychaudhuri S, Stuart JM and Altman RB (2000) Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series, Pacific Symposium on Biocomputing 2000, Honolulu, Hawaii, pp. 452-463.
  • 54
    • 0036139278 scopus 로고    scopus 로고
    • Gene Selection for Sample Classification Based on Gene Expression Data: Study of Sensitivity to Choice of Parameters of the GA/KNN Method
    • Li L, Weinberg CR, Darden TA and Pedersen LG (2001) Gene Selection for Sample Classification Based on Gene Expression Data: Study of Sensitivity to Choice of Parameters of the GA/KNN Method, Bioinformatics, 17, pp. 1131-1142.
    • (2001) Bioinformatics , vol.17 , pp. 1131-1142
    • Li, L.1    Weinberg, C.R.2    Darden, T.A.3    Pedersen, L.G.4
  • 55
    • 0035108235 scopus 로고    scopus 로고
    • A hierarchical unsupervised growing neural network for clustering gene expression patterns
    • Herrero J, Valencia A and Dopazo J (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns, Bioinformatics, 17, pp. 126-136.
    • (2001) Bioinformatics , vol.17 , pp. 126-136
    • Herrero, J.1    Valencia, A.2    Dopazo, J.3
  • 56
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self organizing maps: Methods and applications to hematopoietic differentiation
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES and Golub TR (1999) Interpreting patterns of gene expression with self organizing maps: Methods and applications to hematopoietic differentiation. PNAS, 96, pp. 2907-2912.
    • (1999) PNAS , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 57
    • 0042863923 scopus 로고    scopus 로고
    • Analysis of Gene Expression Data Using Self-organizing Maps
    • Toronen P, Kolehmainen M, Wong G, Castren E (1999) Analysis of Gene Expression Data Using Self-organizing Maps, FEBS letters 451, pp. 142-146.
    • (1999) FEBS letters , vol.451 , pp. 142-146
    • Toronen, P.1    Kolehmainen, M.2    Wong, G.3    Castren, E.4
  • 60
    • 38049058865 scopus 로고    scopus 로고
    • http://cnx.org/content/m11456/latest/
  • 66
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng DF, Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, pp. 351-360.
    • (1987) J. Mol. Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 67
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, vol. 22, No. 22, pp. 4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 68
    • 33751082127 scopus 로고    scopus 로고
    • Chen Y, Pan Y, Chen L, Chen J (2006) Partitioned optimization algorithms for multiple sequence alignment, Proc. of the 20th International Conference on Advanced Information Networking and Applications - (AINA'06), IEEE Computer Society Press, Washington DC., 02, pp. 618-622.
    • Chen Y, Pan Y, Chen L, Chen J (2006) Partitioned optimization algorithms for multiple sequence alignment, Proc. of the 20th International Conference on Advanced Information Networking and Applications - (AINA'06), IEEE Computer Society Press, Washington DC., Volume 02, pp. 618-622.
  • 69
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame C and Higgins DG, SAGA: Sequence alignment by genetic algorithm, Nucleic Acids Research, vol. 24, no. 8, pp. 1515-1524.
    • Nucleic Acids Research , vol.24 , Issue.8 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.G.2
  • 70
    • 0345724917 scopus 로고    scopus 로고
    • Improved hidden Markov model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid
    • Rasmussen TK and Krink T (2003) Improved hidden Markov model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid, BioSystems 72 (2003).
    • (2003) BioSystems , vol.72
    • Rasmussen, T.K.1    Krink, T.2
  • 71
    • 0002297358 scopus 로고
    • Hidden Markov Model induction by Bayesian model merging
    • Stolcke A and Omohundro S (1993) Hidden Markov Model induction by Bayesian model merging. In NIPS 5, pp. 11-18.
    • (1993) NIPS , vol.5 , pp. 11-18
    • Stolcke, A.1    Omohundro, S.2
  • 73
    • 0015808083 scopus 로고
    • Maximum likelihood estimation of evolutionary trees from continuous characters
    • Felsenstein J (1973). Maximum likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Gen. 25: 471-492.
    • (1973) Am. J. Hum. Gen , vol.25 , pp. 471-492
    • Felsenstein, J.1
  • 74
    • 0031892789 scopus 로고    scopus 로고
    • A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data
    • Lewis PO (1998), A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data, Molecular Biology and Evolution, vol. 15, no. 3, pp. 277-283.
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.3 , pp. 277-283
    • Lewis, P.O.1
  • 75
    • 0036679128 scopus 로고    scopus 로고
    • The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
    • Lemmon AR and Milinkovitch MC (2002) The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation, Proc. Natl Acad Sci U S A., vol. 99, no. 16, pp. 10516-10521.
    • (2002) Proc. Natl Acad Sci U S A , vol.99 , Issue.16 , pp. 10516-10521
    • Lemmon, A.R.1    Milinkovitch, M.C.2
  • 79
    • 0043123153 scopus 로고    scopus 로고
    • Vienna rna secondary structure server
    • Hofacker IL (2003) Vienna rna secondary structure server, Nucleic Acids Research, vol. 31:13, pp. 3429-3431.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 80
    • 0024750637 scopus 로고
    • A lattice statistical mechanics model of the conformation and sequence space of proteins
    • Lau KF and Dill KA (1989) A lattice statistical mechanics model of the conformation and sequence space of proteins. Macromolecules 22, pp. 3986-3997.
    • (1989) Macromolecules , vol.22 , pp. 3986-3997
    • Lau, K.F.1    Dill, K.A.2
  • 81
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structures
    • Richards FM (1977) Areas, volumes, packing, and protein structures. Annu. Rev. Biophys. Bioeng. 6, pp. 151-176.
    • (1977) Annu. Rev. Biophys. Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 83
    • 4143144886 scopus 로고    scopus 로고
    • An Improved Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem
    • Shmygelska A, Hoos HH (2003) An Improved Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem. Canadian Conference on AI 2003: 400-417.
    • (2003) Canadian Conference on AI , pp. 400-417
    • Shmygelska, A.1    Hoos, H.H.2
  • 84
    • 25444462754 scopus 로고    scopus 로고
    • An ant colony optimization algorithm for the 2D and 3D hydrophobic polar protein folding problem
    • Shmygelska A, Hoos HH (2005) An ant colony optimization algorithm for the 2D and 3D hydrophobic polar protein folding problem. BMC Bioinformatics 6:30.
    • (2005) BMC Bioinformatics , vol.6 , pp. 30
    • Shmygelska, A.1    Hoos, H.H.2
  • 87
    • 0034869717 scopus 로고    scopus 로고
    • Inference of gene regulatory model by genetic algorithms
    • Ando S and Iba H (2001) Inference of gene regulatory model by genetic algorithms, Proc. Congress on Evolutionary Computation (CEC 2001), vol. 1, pp. 712-719.
    • (2001) Proc. Congress on Evolutionary Computation (CEC , vol.1 , pp. 712-719
    • Ando, S.1    Iba, H.2
  • 88
    • 0031582763 scopus 로고    scopus 로고
    • Trans-gene regulation in adaptive evolution: A genetic algor-ithm model
    • Behera N and Nanjundiah V (1997) Trans-gene regulation in adaptive evolution: A genetic algor-ithm model, Journal of Theoretical Biology, vol. 188, pp. 153-162.
    • (1997) Journal of Theoretical Biology , vol.188 , pp. 153-162
    • Behera, N.1    Nanjundiah, V.2
  • 89
    • 0003329394 scopus 로고    scopus 로고
    • Quantitative Modeling of Gene Regulatory Network - Identifying the Network by Means of Genetic Algorithms
    • Ando S and Iba H (2000) Quantitative Modeling of Gene Regulatory Network - Identifying the Network by Means of Genetic Algorithms, The Eleventh Genome Informatics Workshop, 2000.
    • (2000) The Eleventh Genome Informatics Workshop
    • Ando, S.1    Iba, H.2
  • 93
    • 0036137805 scopus 로고    scopus 로고
    • Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, amber energy functions, and a generalized born/solvent accessibility solvation model
    • Liu Y and Beveridge DL (2002) Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, amber energy functions, and a generalized born/solvent accessibility solvation model. Proteins, 46.
    • (2002) Proteins , vol.46
    • Liu, Y.1    Beveridge, D.L.2
  • 94
    • 38049010096 scopus 로고    scopus 로고
    • Unger R and Moult J (1993) A genetic algorithm for 3d protein folding simulations. In 5th Proc. Intl. Conf. on Genetic Algorithms, pp. 581-588.
    • Unger R and Moult J (1993) A genetic algorithm for 3d protein folding simulations. In 5th Proc. Intl. Conf. on Genetic Algorithms, pp. 581-588.
  • 95
    • 0037343134 scopus 로고    scopus 로고
    • A minimal physically realistic protein-like lattice model: Designing an energy landscape that ensures all-or-none folding to a unique native state
    • Pp
    • Pokarowski P, Kolinski A and Skolnick J (2003) A minimal physically realistic protein-like lattice model: Designing an energy landscape that ensures all-or-none folding to a unique native state. Biophysics Journal, 84: Pp. 1518-26.
    • (2003) Biophysics Journal , vol.84 , pp. 1518-1526
    • Pokarowski, P.1    Kolinski, A.2    Skolnick, J.3
  • 96
    • 0344113807 scopus 로고    scopus 로고
    • Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms
    • Fogel GB and Corne DW Eds, Morgan Kaufmann
    • Kitagawa U and Iba H (2002) Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms, in Evolutionary Computation in Bioinformatics, Fogel GB and Corne DW (Eds.) Morgan Kaufmann.
    • (2002) Evolutionary Computation in Bioinformatics
    • Kitagawa, U.1    Iba, H.2
  • 99
    • 0029275225 scopus 로고
    • Evolutionary Design of Molecules with Desired Properties Using the Genetic Algorithm
    • Venkatasubramanian V, Chan K and Caruthers JM (1995). Evolutionary Design of Molecules with Desired Properties Using the Genetic Algorithm, J. Chem. Inf. Comp. Sci., 35, pp. 188-195.
    • (1995) J. Chem. Inf. Comp. Sci , vol.35 , pp. 188-195
    • Venkatasubramanian, V.1    Chan, K.2    Caruthers, J.M.3
  • 100
    • 0029285723 scopus 로고
    • A Genetic Algorithm for the Automated Generation of Molecule within Constraints
    • Glen RC and Payne AWR (1995) A Genetic Algorithm for the Automated Generation of Molecule within Constraints. J. Computer-Aided Molecular Design, 9, pp. 181-202.
    • (1995) J. Computer-Aided Molecular Design , vol.9 , pp. 181-202
    • Glen, R.C.1    Payne, A.W.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.