Bioinformatics and fuzzy logic

IEEE International Conference on Fuzzy Systems

Volumn , Issue , 2006, Pages 817-824

  Xu, Dong ^a,b   Bondugula, Rajkumar ^b   Popescu, Mihail ^a,c   Keller, James ^a,c  

^a IEEE   (United States)

^b University of Missouri   (United States)

^c UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS PROBLEMS; FUZZY MEASUREMENT; FUZZY SET THEORY;

ALGORITHMS; BIOINFORMATICS; COMPUTATIONAL METHODS; FUZZY LOGIC; FUZZY SETS; PROTEINS;

BIOLOGICAL SYSTEMS;

EID: 34250723225     PISSN: 10987584     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FUZZY.2006.1681805     Document Type: Conference Paper

References (41)

1. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410
2. Q. Leng, Z. Bentwich. (2002) "Beyond self and nonself: fuzzy recognition of the immune system". Scand J Immunol. 56:224-32.
3. J.M. Pedraza, A.van Oudenaarden. (2005) "Noise propagation in gene networks. Science. 307:1965-9.
4. M. Samoilov , S. Plyasunov, A.P. Arkin. (2005) "Stochastic amplification and signaling in enzymatic futile cycles through noiseinduced bistability with oscillations". Proc Natl Acad Sci USA. 102:2310-5.
5. M.S. Steinberg, P.M. McNutt. (1999) "Cadherins and their connections: adhesion junctions have broader functions". Curr Opin CellBiol. Oct;11(5):554-60.
6. R. Sasik, T. Hwa, N. Iranfar, W.F. Loomis. (2001) "Percolation clustering: a novel approach to the clustering of gene expression patterns in Dictyostelium development". Pac Symp Biocomput.:335-47.
7. R. Jansen, M. Gerstein. (2005) "Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction". Curr Opin Microbiol. 7:535-45.
8. The Gene Ontology Consortium: http://www.geneontology.org.
9. M. Popescu, J.M. Keller, J.A. Mitchell. (2005) "Fuzzy Measures on the Gene Ontology for Gene Product Similarity", IEEE Trans. Computational Biology and Bioinformatics, accepted for publication.
10. J.J. Jiang, D.W. Conrath. (1997) "Semantic Similarity Based on Corpus Statistics and Lexical Ontology", Proc. of Int. Conf. Research on Comp. Linguistics X, Taiwan.
11. P. Resnik. (1999) "Semantic similarity in a taxonomy: an information-base measure and its application to problems of ambiguity in natural language", J. of Artificial Intelligence Research (JAIR). 11:95-130.
12. P.W. Lord, R. Stevens, A. Brass, and C.A.Goble. (2003) "Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation". Bioinformatics, 19(10): 1275-83.
13. J. Myllyharju, K.I. Kivirikko,(2004) Trends in Genetics; 20(1), pp. 33-43.
14. N. R. Pal, J. M. Keller, M. Popescu, J.C. Bezdek, J. A. Mitchell and J. Huband.(2005) "Gene ontology-based knowledge discovery through fuzzy cluster analysis", Neural, Parallel and Scientific Computation. 13(3&4), 337-361.
15. N. Speer, C. Spieth, and A. Zell. (2004) "A Memetic Clustering Algorithm for the Functional Partition of Genes Based on the Gene Ontology", Proc. of the 2004 IEEE Symposium on Comp. Intell. in Bioinf. and Comp. Biology (CIBCB 2004), San Diego, California, USA.
16. M. Popescu, J.M. Keller, J.A. Mitchell, and J. Bezdek.(2004) "Functional Summarization of Gene Product Clusters Using Gene Ontology Similarity Measures", Proc. International Conference on Intelligent Sensors, Sensor Networks and Information Processing, Melbourne, Australia, December, 2004.
17. C.A. Joslyn, S.M. Mniszewski, A. Fulmer, and A. Heaton. (2004) "The Gene Ontology Categorizer", Bioinformatics. 20. 1, 69-77.
18. N. Bolshakoval, F. Azuaje and P. Cunningham.(2005) "A knowledgedriven approach to cluster validity assessment", Bioinformatics. 21:10, 2546-2547.
19. A. Ben-Hur, W.S.Noble, (2005) "Kernel methods for predicting protein-protein interactions", Bioinformatics, Vol.21 Suppl. 1, pp i38-i46.
20. P. Khatri, S. Draghici, G.C. Ostermeier, andS.A. Krawetz.(2002) "Profiling gene expression using Onto-Express", Genomics. 79-2, 266-270.
21. T. Andreasen, H. Bulskov, R. Knappe.(2003) "From Ontology over Similarity to Query Evaluation", 2nd CoLogNET-ElsNET Symposium - Questions and Answers: Theoretical and Applied Perspectives. Amsterdam, Holland, 200. 39-50.
22. W.S. Noble, "Support Vector machines applications in computational biology", in Kernel Methods in Computational Biology, B. Schoelkopf, K. Tsuda, J. P. Vert (eds), MIT Press, Cambridge, MA, pp. 71-92.
23. B. Rost. (2001) "Review: protein secondary structure prediction continues to rise". J Struct Biol.134:204-18.
24. J. Meiler, D. Baker. (2003) "Coupled prediction of protein secondary and tertiary structure". Proc Natl Acad Sci.l00:12105-10.
25. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov and P.E. Bourne. (2000) "The Protein Data Bank". Nucleic Acids Res.28:235-242.
26. J. M. Keller, M. R. Gray and J. A. Givens, Jr. (1985) "A fuzzy K-Nearest Neighbor Algorithm". IEEE Trans, on SMC, Volume SMC-15, No.4.
27. S.F. Altschul, T.L Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J Lipman. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Res. 25:3389-3402.
28. A. A. Salamov and V. V. Solovyev. (1995) "Prediction of Protein Secondary Structure by Combining Nearest-neighbor Algorithm and Multiple Sequence Alignments". J. Mol. Biol., 247:11-15.
29. J. Sim, S.Y. Kim, J. Lee. (2005) "Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method". Bioinformatics. 2005 Jun 15;21(12):2844-9. Epub Apr 6.
30. Y. Huang, Y. Li. (2004) "Prediction of protein subcellular locations using fuzzy k-NN method". Bioinformatics. Jan 1;20(l):21-8.
31. B.C. Chang, S.K. Halgamuge. (2002) "Protein motif extraction with neuro-fuzzy optimization". Bioinformatics. Aug;18(8):1084-90.
32. W.R. Atchley, A.D. Fernandes. Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network. Proc Natl Acad Sci USA. 2005 May 3;102(18):6401-6. Epub 2005 Apr 25.
33. L. Pickert, I. Reuter, F. Klawonn, E. Wingender.(1998) "Transcription regulatory region analysis using signal detection and fuzzy clustering". Bioinformatics. 14(3):244-51.
34. T. V. Arredondo, P.S. Neelakanta, D. De Groff. (2005) "Fuzzy attributes of a DNA complex: development of a fuzzy inference engine for codon-"junk" codon delineation". Artif Intell Med. 2005 Sep-Oct;35(1-2):87-105.
35. A. Torres, J.J. Nieto. (2003) "The fuzzy polynucleotide space: basic properties". Bioinformatics. Mar 22;19(5):587-92.
36. K. Sadegh-Zadeh. (2000) "Fuzzy genomes". Artif Intell Med. Jan;18(1):1-28.
37. E. Jacob, R. Sasikumar, K.N. Nair. (2004) "A fuzzy guided genetic algorithm for operon prediction". Bioinformatics. 2005 Apr 15;21(8):1403-7. Epub Nov 25.
38. T.R. Cundari, Russo M. Database mining using soft computing techniques. (2001) "An integrated neural network-fuzzy logic-genetic algorithm approach". J Chem Inf Comput Sci. Mar-Apr;41(2):281-7.
39. J.L. Jenkins, M. Glick, J.W. Davies. (2004) "A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes". J Med Chem. 2004 Dec 2;47(25):6144-59.
40. R. Blankenbecler, M. Ohlsson, C Peterson, M. Ringner. (2003) "Matching protein structures with fuzzy alignments". Proc Natl Acad Sci USA. 2003 Oct 14;100(21):11936-40. Epub Oct 2.
41. Z. Sun, X. Xia, Q. Quo, and D. Xu.(1999) "Protein structure prediction in a 210-type lattice model: parameter optimization in the genetic algorithm using orthogonal array". Journal of Protein Chemistry. Jan;18(1):39-46