Protein classification using probabilistic chain graphs and the Gene Ontology structure

Bioinformatics

Volumn 22, Issue 15, 2006, Pages 1871-1878

  Carroll, Steven ^a   Pavlovic, Vladimir ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLASSIFICATION; GENE INTERACTION; GENE STRUCTURE; GENETIC DATABASE; INTERMETHOD COMPARISON; MATHEMATICAL MODEL; MOLECULAR MODEL; PLOTS AND CURVES; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; REPLICATION STUDY; SACCHAROMYCES;

SACCHAROMYCES;

EID: 33747856187     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl187     Document Type: Article

References (23)

1. Breitkreutz,B.J. et al. (2003) The GRID: The general repository for interaction datasets. Gen. Biol., 4, R23.
2. Ashburner,M. et al. (2000) Geneontology: Tool for the unification of biology. The gene ontology consortium. Nat. Gen., 25, 25-29.
3. Drawid,A. and Gerstein,M. (2000) A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol., 301, 1059-1075.
4. Deng,M., Zhang,K., Mehta,S., Chen,T. and Sun,F. (2002) Prediction of protein function using protein-protein interaction data. In Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB2002). Standford University, Palo Alto, CA, pp. 197-206.
5. Deng,M., Chen,T. and Sun,F. (2003) An integrated probabilistic model for functional prediction of proteins. In Proceedings of the Seventh International Conference on Computational Molecular Biology (RECOMB2003), Berlin, Germany, pp. 95-103.
6. Deng,M. et al. (2004) Mapping gene ontology to proteins based on protein-protein interaction data. Bioinformatics, 20, 895-902.
7. Galperin,M.Y. and Koonin,E.V. (2000) Who's your neighbor? New computational approaches for functional genomics Nat. Biotechnol., 18, 609-613.
8. Geman,S. and Geman,D. (1984) Stochastic relaxation,Gibbs distribution and the Bayesian restoration of images. IEEE Trans. Pattern Anal. Mach. Intell., 6, 721-741.
9. Iyer,L.M. et al. (2001) Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol., 2, RESEARCH0051.
10. Koonin,E.V. (2001) Computational genomics. Curr. Biol., 11, R155-R1558.
11. Lauritzen,S.L. (1996) Graphical Models. Oxford University Press, New York, NY.
12. Letovsky,S. and Kasif,S. (2003) Predicting protein function from protein/ protein interaction data: A probabilistic approach. Bioinformatics, 19 (Suppl), i197-i204.
13. Liu,J. and Rost,B. (2001) Comparing function and structure between entire proteomes. Prot. Sci., 10, 1970-1979.
14. Liu,J. and Rost,B. (2003) CHOP proteins into structural domain-like fragments. J. Mol. Biol., (submitted 2003-03-25).
15. Nakai,K. and Horton,P. (1999) PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. TIBS, 24, 34-36.
16. Nair,R., Carter,P. and Rost,B. (2003) NLSdb: Database of nuclear localization signals. Nucleic Acids Res., 31, 397-399.
17. Neapolitan,R.E. (2004) Learning Bayesian Networks. Prentice-Hall, Upper Saddle River, NJ.
18. Pearl,J. (1988) Probabilistic reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann.
19. Pruess,M. et al. (2003) The Proteome Analysis database: A tool for the in silico analysis of whole proteomes. Nucleic Acids Res., 31, 414-417.
20. Rost,B. (2003) Automatic prediction of protein function. Cellular Molecular Life Sciences, 60, 2637-2650.
21. Valencia,A. and Pazos,F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol., 12, 368-373.
22. Whisstock,J.C. and Lesk,A.M. (2003) Prediction of protein function from protein sequence and structure. Quart. Rev. Biophys., 36, 307-340.
23. Yedidia,J.S., Freeman,W.T. and Weiss,Y. Understanding belief propagation and its generalizations. Technical Report TR2001-22, Mitsubishi Electric Research Labs, January 2002.