Biclustering of microarray data with MOSPO based on crowding distance

BMC Bioinformatics

Volumn 10, Issue SUPPL. 4, 2009, Pages

  Liu, Junwan ^a,b   Li, Zhoujun ^a,c   Hu, Xiaohua ^d   Chen, Yiming ^a,e  

^a NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

^b CENTRAL SOUTH UNIVERSITY OF FORESTRY AND TECHNOLOGY   (China)

^c BEIHANG UNIVERSITY   (China)

^d DREXEL UNIVERSITY   (United States)

^e HUNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DIVERSITY OF SOLUTIONS; EXPERIMENTAL CONDITIONS; GENE EXPRESSION DATASETS; GENE EXPRESSION PROFILES; HEURISTIC SEARCH TECHNIQUE; MICROARRAY TECHNOLOGIES; MULTI OBJECTIVE PARTICLE SWARM OPTIMIZATION; NEAREST NEIGHBOUR SEARCH;

DATA REDUCTION; DIAGNOSIS; HEURISTIC ALGORITHMS; ISOMERS; MATRIX ALGEBRA;

GENE EXPRESSION;

CONFERENCE PAPER; GENE CLUSTER; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC DISTANCE; GENETIC MODEL; HUMAN; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; SPECIES DIFFERENCE; ALGORITHM; ARTICLE; CLUSTER ANALYSIS; DNA MICROARRAY; METHODOLOGY;

AVES;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 65449117238     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S9     Document Type: Conference Paper

References (37)

1. Su A Cooke M Ching K Hakak Y Walker J Wiltshire T Orth A Vega R Sapinoso L Moqrich A Large-scale analysis of the human and mouse transcriptomes Proc Natl Acad Sci U S A 2002, 99:4465-4470. 123671 11904358
2. De Smet F Mathys J Marchal K Thijs G De Moor B Moreau Y Adaptive quality-based clustering of gene expression profiles Bioinformatics 2002, 18:735-746. 12050070
3. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1998, 95:14863-14868. 24541 9843981
4. Tamayo P Slonim D Mesirov J Zhu Q Kitareewan S Dmitrovsky E Lander ES Golub TR Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation Proc Natl Acad Sci USA 1999, 96:2907-2912. 15868 10077610
5. Cheng Y Church GM Biclustering of expression data Proc Int Conf Intell Syst Mol Biol 2000, 8:93-103. 10977070
6. Wang H Wang W Yang J Yu PS Clustering by pattern similarity in large data sets Proceedings of the 2002 ACM SIGMOD international conference on Management of data 2002:394-405.
7. Tanay A Sharan R Shamir R Discovering statistically significant biclusters in gene expression data Bioinformatics 2002, 18(Suppl 1):S136-144. 12169541
8. Dhillon IS Co-clustering documents and words using bipartite spectral graph partitioning Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining 2001:269-274.
9. Sheng Q Moreau Y De Moor B Biclustering microarray data by Gibbs sampling Bioinformatics 2003, 19(Suppl 2):iI196-205. 14534190
10. Bryan K Cunningham P Bolshakova N Coll T Dublin I Biclustering of expression data using simulated annealing Computer-Based Medical Systems, 2005. Proceedings. 18th IEEE Symposium on 2005:383-388.
11. Madeira SC Oliveira AL Biclustering algorithms for biological data analysis: A survey IEEE/ACM Trans Comput Biol Bioinform 2004, 1:24-45. 17048406
12. Deb K Multi-Objective Optimization Using Evolutionary Algorithms John Wiley & Sons, Chichester 2001.
13. Deb K Pratap A Agarwal S Meyarivan T A fast and elitist multiobjective genetic algorithm: NSGA-II Evolutionary Computation, IEEE Transactions on 2002, 6:182-197.
14. Knowles J Corne D Approximating the Nondominated Front Using the Pareto Archived Evolution Strategy Evolutionary Computation 2000, 8:149-172. 10843519
15. Zitzler E Laumanns M Thiele L SPEA2: Improving the Strength Pareto Evolutionary Algorithm EUROGEN 2001, 95:100.
16. Laumanns M Thiele L Deb K Zitzler E Combining Convergence and Diversity in Evolutionary Multiobjective Optimization Evolutionary Computation 2002, 10:263-282. 12227996
17. Mitra S Banka H Multi-objective evolutionary biclustering of gene expression data Pattern Recognition 2006, 39:2464-2477.
18. Divina F Aguilar-Ruiz JS A multi-objective approach to discover biclusters in microarray data Proceedings of the 9th annual conference on Genetic and evolutionary computation 2007:385-392.
19. Kennedy J Eberhart RC Particle swarm optimization Proceedings, IEEE International Conference on Neural Networks 1995:1942-1948.
20. Kennedy J Eberhart RC A discrete binary version of the particle swarm algorithm Proceedings of IEEE Conference on Systems, Man, and Cybernetics 1997:4104-4109.
21. Mostaghim S Teich J Strategies for finding good local guides in multi-objective particle swarm optimization (MOPSO) Swarm Intelligence Symposium, 2003. SIS'03. Proceedings of the 2003 IEEE 2003:26-33.
22. Parsopoulos KE Vrahatis MN Particle swarm optimization method in multiobjective problems Proceedings of the 2002 ACM Symposium on Applied Computing (SAC'2002) 2003:603-607.
23. Mostaghim S Teich J The Role of - dominance in Multi Objective Particle Swarm Optimization Methods Proceedings of the 2003 Congress on Evolutionary Computation (CEC 2003), Camberra Australia, IEEE Press 2003:1764-1771.
24. Sierra MR Coello CAC Improving PSO-Based Multi-objective Optimization Using Crowding, Mutation and e-Dominance Proceedings of the Third International Conference on Evolutionary Multi-Criterion Optimization (EMO 2005) 2005:505-519.
25. Raquel C Naval P Jr An effective use of crowding distance in multiobjective particle swarm optimization Proceedings of the 2005 conference on Genetic and evolutionary computation 2005:257-264.
26. Srinivisan D Seow TH Particle swarm inspired evolutionary algorithm (PS-EA) for multiobjective optimization problem Proceedings of Congress on Evolutionary Computation (CEC-2003) 2003:2292-2297.
27. Ray T Liew K A Swarm Metaphor for Multiobjective Design Optimization Engineering Optimization 2002, 34:141-153.
28. Li X A Non-dominated Sorting Particle Swarm Optimizer for Multiobjective Optimization LECTURE NOTES IN COMPUTER SCIENCE 2003:37-48.
29. Reyes-Sierra M Coello CAC Multi-Objective Particle Swarm Optimizers: A Survey of the State-of-the-Art International Journal of Computational Intelligence Research 2006, 2:287-308.
30. Liu JW Li ZJ Liu FF Chen YM Multi-Objective Particle Swarm Optimization Biclustering of Microarray Data IEEE International Conference on Bioinformatics and Biomedicine(BIBM 2008) 2008:363-366.
31. Khatri P Draghici S Ostermeier G Krawetz S Profiling Gene Expression Using Onto-Express Genomics 2002, 79:266-270. 11829497
32. Tavazoie S Hughes JD Campbell MJ Cho RJ Church GM Systematic determination of genetic network architecture Nature Genetics 1999, 22:281-285. 10391217
33. Divina F Aguilar-Ruiz JS Biclustering of expression data with evolutionary computation IEEE transactions on knowledge and data engineering 2006, 18:590-602.
34. Zhang X-h Meng H-y Jiao L-c Intelligent particle swarm optimization in multiobjective optimization Congress on Evolutionary Computation (CEC'2005) IEEE Press, Edinburgh, Scotland, UK 2005:714-719.
35. Cho RJ Campbell MJ Winzeler EA Steinmetz L Conway A Wodicka L Wolfsberg TG Gabrielian AE Landsman D Lockhart DJ A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle Molecular Cell 1998, 2:65-73. 9702192
36. Alizadeh AA Eisen MB Davis RE Ma C Lossos IS Rosenwald A Boldrick JC Sabet H Tran T Yu X Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 2000, 403:503-511. 10676951
37. Yang J Wang W Wang H Yu P δ-clusters: Capturing subspace correlation in a large dataset Data Engineering, 2002. Proceedings. 18th International Conference on 2002:517-528.