AutoClass@IJM: A powerful tool for Bayesian classification of heterogeneous data in biology

Nucleic Acids Research

Volumn 37, Issue SUPPL. 2, 2009, Pages

  Achcar, Fiona ^a,b   Camadro, Jean michel ^b   Mestivier, Denis ^a  

^a 'Modeling in Integrative Biology' Group   (France)

^b INSTITUT JACQUES MONOD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION SERVICE PROVIDER; ARTICLE; AUTOMATION; BAYESIAN LEARNING; BIOINFORMATICS; COMMUNICATION SOFTWARE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER SYSTEM; DATA ANALYSIS; DATA MINING; GENETIC DATABASE; HUMAN; HUMAN COMPUTER INTERACTION; INFORMATION TECHNOLOGY; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; MICROCOMPUTER; NONHUMAN; PRIORITY JOURNAL; WEB BROWSER;

ALGORITHMS; BAYES THEOREM; CLASSIFICATION; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 67849111567     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp430     Document Type: Article

References (31)

1. Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
2. Gollub,J. and Sherlock,G., (2006). Clustering microarray data. Methods Enzymol., 411, 194-213.
3. De Hoon,M.J., Imoto,S., Nolan,J. and Miyano,S. (2004) Open source clustering software. Bioinformatics, 20, 1453-1454.
4. Dembele,D. and Kastner,P. (2003). Fuzzy c-means method for clustering microarray data. Bioinformatics, 19, 973-980.
5. Kraj,P., Sharma,A., Garge,N., Podolsky,R. and Mcindoe,R.A. (2008) Parakmeans: Implementation of a parallelized k-means algorithm suitable for general laboratory use. BMC Bioinformatics, 9, 200.
6. Medvedovic,M. and Sivaganesan,S., (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics, 18, 1194-1206.
7. Medvedovic,M., Yeung,K.Y. and Bumgarner,R.E. (2004) Bayesian mixture model based clustering of replicated microarray - data. Bioinformatics, 20, 1222-1232.
8. Yeung,K.Y., Fraley,C., Murua,A., Raftery,A.E. and Ruzzo,W.L. (2001) Model-based clustering and data transformations for gene expression data. Bioinformatics, 17, 977-987.
9. Ng,S.K., Mclachlan,G.J., Wang,K., Ben-tovim Jones,L. and Ng,S.W. (2006) A mixture model with random-effects components for clustering correlated gene-expression profiles. Bioinformatics, 22, 1745-1752.
10. Qin,Z.S. (2006) Clustering microarray gene expression data using weighted chinese restaurant process. Bioinformatics, 22, 1988-1997.
11. Xiang,Z., Qin,Z.S. and He,Y. (2007) Crcview: A web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinformatics, 23, 1843-1845.
12. Fraley,C. and Raftery,A.E. (1998) How many clusters? Which clustering method? Answers via model-based cluster analysis. Comput. J., 41, 578-588.
13. Haughton,D., Legrand,P. and Woolford,S. (2009) Review of three latent class cluster analysis packages: Latent gold, polca, and mclust. Am. Statistician, 63, 81-91.
14. Tadesse,M.G., Sha,N. and Vannucci,M. (2005) Bayesian variable selection in clustering high-dimensional data. J. Am. Stat. Assoc., 100 602-617.
15. Baladandayuthapani,V., Mallick,B.K., Hong,M.Y., Lupton,J.R., Turner,N.D. and Carroll,R.J. (2008) Bayesian hierarchical spatially correlated functional data analysis with application to colon carcinogenesis. Biometrics, 64, 64-73.
16. Cheeseman,P., Kelly,J., Self,M., Stutz,J., Taylor,W. and Freeman,D. (1988). AutoClass: A Bayesian Classification System, in Proceedings of the Fifth International Conference on Machine Learning. Morgan Kaufmann Publishers, San Francisco.
17. Cheeseman,P. and Stutz,J. (1996) Bayesian Classification (AutoClass): Theory and Results. In Fayyad,U., Piatelsky- Shapiro,G., Smyth,P. and Uthurusamy,R. (eds), Advances in Knowledge Discovery and Data Mining AAAI Press/MIT Press, Cambridge.
18. Moter,E.J., Radisky,D.C. and Mian,I.S. (2000) Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in S. Cerevisiae. Physiol. Genomics, 4, 127-135.
19. Chow,M.L., Moter,E.J. and Mian,I.S. (2001) Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol. Genomics, 5, 409-111.
20. Semeiks,J.R., Grate,L.R. and Mian,I.S. (2005) Text-based analysis of genes, proteins, aging, and cancer. Mech. Ageing Dev., 126, 193-208.
21. Semeiks,J.R., Rizki,A., Bissell,M.J. and Mian,I.S. (2006) Ensemble attribute profile clustering: Discovering and characterizing groups of genes with similar patterns of biological features. BMC Bioinformatics, 7, 147.
22. Hunter,L. and States,D. (1992) Bayesian classification of protein structure. IEEE Intell. Sys., 7, 67-75.
23. Okada,Y., Sahara,T., Mitsubayashi,H., Ohgiya,S. and Nagashima,T. (2005) Knowledge-assisted recognition of cluster boundaries in gene expression data. Artif. Intell. Med., 35, 171-183.
24. Crook,A.C., Baddeley,R. and Osorio,D. (2002) Identifying the structure in cuttlefish visual signals. Philos. Trans. R. Soc. Lond. B. Biol. Sci., 357, 1617-1624.
25. Rasmussen,M.D., Deshpande,M.S.,Karypis,G., Johnson,J., Crow,J.A. and Retzel,E.F. (2003) Wcluto: A web-enabled-clustering toolkit. Plant Physiol., 133, 510-516.
26. Saldanha,A.J. (2004) Java Treeview - extensible visualization of microarray data. Bioinformatics, 20, 3246-3248.
27. Weng,S., Dong,Q., Salakrishnan,R., Christie,K., Costanzo,M., Dolinski,K., Dwight,S.S., Engel,S., Fisk,D.G., Hong,E. et al. (2003) Saccharomypes Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 31, 216-218.
28. Yoshimoto,H., Saltsman,K., Gasch,A.P., Li,H.X., Ogawa,N., Botstein,D., Brown,P.O. and Cyert,M.S. (2002) Genome-wide analysis of gene expression regulated by the calcineurin/Crzlp signaling pathway in Saccharomyces Cerevisiae. J. Biol. Chem., 277, 31079-31088.
29. Bailey,T.L., Williams,N., Misleh,C. and Li,W.W. (2006) MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34, W369-W373.
30. Beer,M.A. and Tavazoie,S. (2004) Predicting gene expression from sequence. Cell, 117, 185-198.
31. Pizzuti,C. and Talia,D. (2003) P-autoclass: Scalable parallel clustering for mining large data sets. IEEE. Trans. Knowledg Data Eng., 15 629-641.