Discovery of microRNA-mRNA modules via population-based probabilistic learning

Bioinformatics

Volumn 23, Issue 9, 2007, Pages 1141-1147

  Joung, Je Gun ^a   Hwang, Kyu Baek ^b   Nam, Jin Wu ^a   Kim, Soo Jin ^a   Zhang, Byoung Tak ^a,c  

^a Seoul National University   (South Korea)

^b Soongsil University   (South Korea)

^c Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ARTICLE; CORRELATION ANALYSIS; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE TARGETING; GENETIC ANALYSIS; HUMAN; INFORMATION SYSTEM; LEARNING ALGORITHM; MALIGNANT NEOPLASTIC DISEASE; PRIORITY JOURNAL; PROBABILITY; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BINDING SITE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; SEQUENCE ANALYSIS;

ARTIFICIAL INTELLIGENCE; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETICS, POPULATION; MICRORNAS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA;

EID: 34249849395     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm045     Document Type: Article

References (35)

1. Akasaka,T. et al. (2003) BCL6 gene translocation in follicular lymphoma: A harbinger of eventual transformation to diffuse aggressive lymphoma. Blood, 102, 1443-1448.
2. Baluja,S. (1994) Population-Based incremental learning a method for integrating genetic search Based function optimization and competitive learning. Technical Report CMU-CS-94-163, Carnegie Mellon University, Pittsburgh.
3. Baluja,S. (1997) Genetic algorithms and explicit search statistics. Adv. Neural Inf. Process. Syst., 9, 3l9-325.
4. Bartel,D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
5. Calin,G.A. et al. (2004) Human microRNA genes are-frequently located at fragile sites and genomic regions involved in cancers. PNAS, 101, 2999-3004.
6. Chen,D. et al. (2005) ARF-BP1/Mule is a critical mediator of the ARF tumor suppressor. Cell, 121, 1071-1083.
7. Cheng,Y. and Church,G. (2000) Biclustering of expression data. In Proceedings of ISMB. pp. 93-103.
8. Deb,K. (2001) Multi-Objective Optimization Using Evolutionary Algorithms. Chichester Wiley, UK.
9. Denli,A.M. et al. (2004) Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231-235.
10. Donsante,A. et al. (2001) Observed incidence of tumorigenesis in long-term rodent studies of rAAV vectors. Gene The., 8, 1343-1346.
11. Fonseca,C.M. and Fleming,P.J. (1993) Genetic algorithms for multiobjective optimization: Formulation, discussion and generalization. In Proceedings of ICGA, pp. 416-423.
12. Griffiths-Jones,S. et al. (2006) miRBase: MicroRNA sequences, targets and gene nomenclature. Nucl. Acids Res., 34, D140-D144.
13. Han,J. et al. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell, 125, 887-901.
14. Huang,J.C. et al. (2006) Detecting microRNA targets by linking sequence, microRNA and gene expression data. In Proceedings of RECOMB pp. 114-129.
15. Johnson,S.M. et al. (2005) RAS is regulated by the let-7 microRNA family. Cell, 120, 635-647.
16. Joung,J.-G. et al. (2006) Identification of regulatory modules by co-clustering latent variable models: Stem cell differentiation. Bioinformatics, 22, 2005-2011.
17. Jung,B. et al. (2004) Loss of activin receptor type 2 protein expression in microsatellite unstable colon cancers. Gastroenterology 126, 654-659.
18. Larrañaga,P. and Lozano,J.A. (2002) Estimation of Distribution Algorithms: A New Tool for Evolutionary Computation. Kluwer Academic Publishers.
19. Lewis,B.P. et al. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
20. Liu,C.G. et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. PNAS, 101, 9740-9744.
21. Lu,J. et al. (2005) MicroRNA expression profiles classify human cancers. Nature, 435, 834-838.
22. Madeira,S.C. and Oliveira,A.L. (2004) Biclustering algorithms for biological data analysis: A survey. IEEE/ACM Trans. Comput. Biol. Bioinform., 1, 24-45.
23. Myllykangas,S. et al. (2006) DNA copy number amplification profiling of human neoplasms. Oncogene, 25, 7324-7332.
24. Nam,J.-W. et al. (2006) ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. Nucl. Acids Res., 34, W455-W458.
25. Ohl,F. et al. (2005) Gene expression studies in prostate cancer tissue: Which reference gene should be selected for normalization? J. Mol. Med., 83, 1014-1024.
26. Pagano,M. (1997) Cell cycle regulation by the ubiquitin pathway. FASEB J., 11, 1067-1075.
27. Potter,M.A. and De Jong,K.A. (2000) Cooperative coevolution: An architecture for evolving coadapted subcomponents. Evol. Comput., 8, 1-29.
28. Saito,Y. et al. (2006) Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell, 9, 435-443.
29. Thomson,J.M. et al. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat. Methods, 1, 47-53.
30. Yekta,S. et al. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
31. Yoon,S. and De Micheli,G. (2005) Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics, 21, ii93-ii100.
32. Zaritsky,A. and Sipper,M. (2004). Coevolving solutions to the shortest common superstring problem. BioSystems, 76, 209-216.
33. Zhang,B.-T. (2003) A unified Bayesian framework for evolutionary learning and optimization. In Advances in Evolutionary Computation Chapter 15. Springer-Verlag, pp. 393-412.
34. Zilberstein,C.B.-Z. et al. (2006) A high-throughput approach for associating microRNAs with their activity conditions. J. Comput. Biol., 13, 245-266.
35. Zou,H. et al. (2002) Anaphase specific auto-cleavage of separase. FEBS Lett., 528, 246-250.