A novel approach for mining and fuzzy simulation of subnetworks from large biomolecular networks

IEEE Transactions on Fuzzy Systems

Volumn 15, Issue 6, 2007, Pages 1219-1229

  Hu, Xiaohua ^a   Sokhansanj, Bahrad ^b   Wu, Daniel ^a   Tang, Yuchun ^c,d  

^a Drexel University   (United States)

^b DREXEL UNIVERSITY   (United States)

^c GEORGIA STATE UNIVERSITY   (United States)

^d Secure Computing Corporation   (United States)

Author keywords

Biomedical literature mining; Biomolecular networks; Data mining; Fuzzy logic; Information extraction; Information resources; Literature; Medical information systems; Search problems; Subnetwork

Indexed keywords

BIOMOLECULES; DYNAMIC MODELS; FUZZY LOGIC; FUZZY RULES; GENES; INFORMATION SYSTEMS; MICROARRAYS;

BIOMOLECULAR NETWORK; CELLULAR FUNCTION; INFORMATION EXTRACTION; MEDICAL INFORMATION SYSTEMS;

DATA MINING;

EID: 34547737034     PISSN: 10636706     EISSN: None     Source Type: Journal    
DOI: 10.1109/TFUZZ.2007.896248     Document Type: Article

References (55)

1. J. P. Fitch and B. Sokhansanj, "Genomic engineering: Moving beyond DNA sequence to function," Proc. IEEE, vol. 88, no. 12, pp. 1949-1971, Dec. 2000.
2. P. D'haeseleer, S. Liang, and R. Somogyi, "Genetic network inference: From co-expression clustering to reverse engineering," Bioinformatics, vol. 16, no. 8, pp. 707-726, Apr. 2000.
3. L. Glass and S. A. Kauffman, "The logical analysis of continuous non-linear biochemical control: Networks," J. Theor. Biol., vol. 39, no. 1, pp. 103-129, Apr. 1973.
4. J. Tegnér, M. K. S. Yeung, J. Hasty, and J. J. Collins, "Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling," Proc. Nat. Acad. Sci. USA, vol. 100, no. 10, pp. 5944-5949, May 2003.
5. L. A. Zadeh, "Fuzzy sets," Inf. Contr., vol. 8, no. 3, pp. 338-353, Jun. 1965.
6. L. Hirschman, J. C. Park, J. Tsujil, L. Wong, and C. H. Wu, "Accomplishments and challenges in literature data mining for biology," Bioinformatics, vol. 18, no. 12, pp. 1553-1561, Dec. 2002.
7. T. Hasegawa, S. Sekine, and R. Grishman, "Discovering relations among named entities from large corpora," in Proc. Annu. Meeting Assoc. Comput. Linguist., Barcelona, Spain, Jul. 21-26, 2004, pp. 415-422.
8. K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi, "Toward information extraction: Identifying protein names from biological papers," in Proc. Pac. Symp. Biocomput., Jan. 1998, pp. 707-718.
9. B. J. Stapley and G. Benoit, "Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in medline abstracts," in Proc. Pac. Symp. Biocomput., Jan. 2000, pp. 529-540.
10. C. Blaschke, M. A. Andrade, C. Ouzounis, and A. Valencia, "Automatic extraction of biological information from scientific text: Protein-protein interactions," in Proc. Int. Conf. Intell. Syst. Mol. Biol., Heidelberg, Germany, Aug. 6-10, 1999, pp. 60-67.
11. J. H. Chiang and H. H. Yu, "MeKE: Discovering the functions of gene products from biomedical literature via sentence alignment," Bioinformatics, vol. 19, no. 11, pp. 1417-1422, Jul. 2003.
12. B. de Brujin and J. Martin, "Literature mining in molecular biology," in Proc. EFMI Workshop Natural Lang., Nicosia, Cyprus, Mar. 8-9, 2002, pp. 1-5.
13. T. Ono, H. Hishigaki, A. Tanigami, and T. Takagi, "Automated extraction of information on protein-protein-interactions from the biological literature," Bioinformatics, vol. 17, no. 2, pp. 155-161, Feb. 2001.
14. E. Marcotte, I. Xenarios, and D. Eisenberg, "Mining literature for protein interactions," Bioinformatics, vol. 17, no. 4, pp. 359-363, Apr. 2001.
15. U. Hahn, M. Romacker, and S. Schulz, "Creating knowledge repositories from biomedical reports: The MEDSYNDIKATE text mining system," in Proc. Pac. Symp. Biocomput., Jan. 2002, pp. 338-349.
16. M. E. J. Newman, "The structure and function of complex networks," SIAM Rev., vol. 45, no. 2, pp. 167-256, 2003.
17. R. F. Hashimoto, S. Kim, I. Shmulevich, W. Zhang, M. L. Butner, and E. R. Dougherty, "Growing genetic regulatory networks from seed genes," Bioinformatics, vol. 20, no. 8, pp. 1241-247, May 2004.
18. G. W. Hake, S. R. Lawrence, C. L. Giles, and F. M. Coetzee, "Self-organization and identification of web communities," IEEE Computer, vol. 35, pp. 66-71, Mar. 2002.
19. R. Jansen, N. Lan, J. Qian, and M. Gerstein, "Integration of genomic datasets to predict protein complexes in yeast," J. Struct. Funct. Genomics, vol. 2, no. 2, pp. 71-81, 2002.
20. G. D. Bader and C. W. V. Hogue, "An automated method for finding molecular complexes in large protein interaction networks," BMC Bioinformatics, vol. 4, no. 2, Jan. 2003.
21. D. Bu, Y. Zhao, L. Cai, H. Xue, X. Zhu, H. Lu, J. Zhang, S. Sun, L. Ling, N. Zhang, G. Li, and R. Chen, "Topological structure analysis of the protein-protein interaction network in budding yeast," Nucl. Acids Res., vol. 31, no. 9, pp. 2443-2450, May 2003.
22. X. Hu, "Mining and analysing scale-free protein-protein interaction network," Int. J. Bioinformatics Res. Applicat., vol. 1, no. 1, pp. 81-101, 2005.
23. X. Hu, I. Yoo, I.-Y. Song, M. Song, J. Han, and M. Lechner, "Extracting and mining protein-protein interaction network from biomedical literature," in Proc. 2004 IEEE Symp. Comput. Intell. Bioinformatics Comput. Biol., San Diego, CA, Oct. 7-8, 2004, pp. 244-251.
24. L. H. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray, "From molecular to modular cell biology," Nature, vol. 402, no. 6761 Suppl., pp. C47-C52, Dec. 1999.
25. V. Spirin and L. A. Mirny, "Protein complexes and functional modules in molecular networks," Proc. Nat. Acad. Sci. USA, vol. 100, no. 21, pp. 12123-12128, Oct. 2003.
26. A. W. Rives and T. Galitski, "Modular organization of cellular networks," Proc. Nat. Acad. Sci. USA, vol. 100, no. 3, pp. 1128-1133, Feb. 2003.
27. R. A. Rosales, M. Fill, and A. L. Escobar, "Calcium regulation of single ryanodine receptor channel gating analyzed using HMM/MCMC statistical methods," J. Gen. Physiol., vol. 121, pp. 533-553, 2004.
28. A. Schliep, A. Schonhuth, and C. Steinholf, "Using hidden Markov models to analyze gene expression time course data," Bioinformatics, vol. 19, no. Suppl. 1, pp. i255-i263, Jul. 2003.
29. C. Rangel, J. Angus, Z. Ghahramani, M. Lioumi, E. Sotheran, A. Gaiba, D. L. Wild, and F. Falciani, "Modeling T-cell activation using gene expression profiling and state-space models," Bioinformatics, vol. 20, no. 9, pp. 1361-1372, Jun. 2004.
30. M. J. Beal, F. Falciani, Z. Ghahramani, C. Rangel, and D. L. Wild, "A Bayesian approach to reconstructing genetic regulatory networks with hidden factors," Bioinformatics, vol. 21, no. 3, pp. 349-356, Feb. 2004.
31. I. Nachman, A. Regev, and N. Friedman, "Inferring quantitative models of regulatory networks from expression data," Bioinformatics, vol. 20, no. Suppl 1, pp. i248-i256, Aug. 2004.
32. P. D'Haeseleer, X. Wen, S. Fuhrman, and R. Somogyi, "Linear modeling of mRNA expresion levels during CNS development and injury," in Proc. Pac. Symp. Biocomput., Jan. 1999, pp. 41-52.
33. R. Laubenbacher and B. Stigler, "A computational algebra approach to the reverse-engineering of gene regulatory networks," J. Theor. Biol., vol. 229, no. 4, pp. 523-537, Aug. 2004.
34. I. Shmulevich, E. R. Dougherty, S. Kim, and W. Zhang, "Probabilistic boolean networks: A rule-based uncertainty model for gene regulatory networks," Bioinformatics, vol. 18, no. 2, pp. 261-274, Feb. 2002.
35. T. J. Perkins, M. Hallett, and L. Glass, "Inferring models of gene expression dynamics," J. Theor. Biol., vol. 230, no. 3, pp. 289-299, Oct. 2004.
36. X. Hu and D. Wu, "Data mining and predictive modeling of biomolecular network from biomedical literature databases," IEEE/ACM Trans. Comp. Biol. Bioinf., to be published.
37. M. Girvan and M. E. J. Newman, "Community structure in social and biological networks," Proc. Nat. Acad. Sci. USA, vol. 99, no. 12, pp. 7821-7826, June 2002.
38. M. E. J. Newman and M. Girvan, "Finding and evaluating community structure in networks," Phys. Rev. E, vol. 69, no. 2, 026113, Feb. 2004.
39. M. E. J. Newman, "Fast algorithm for detecting community structure in networks," Phys. Rev. E, vol. 69, no. 6, 066133, Jun. 2004.
40. L. Donetti and M. A. Munoz, "Detecting network communities: A new systematic and efficient algorithm," J. Stat. Mech., no. 10, p. 10012, Oct. 2004.
41. S. White and P. Smyth, "A spectral clustering approach to finding communities in graph," in Proc. SIAM Int. Conf. Data Mining, Newport Beach, CA, Apr. 2005.
42. P. Holme, M. Huss, and H. Jeong, "Subnetwork hierarchies of biochemical pa thways," Bioinformatics, vol. 19, no. 4, pp. 532-538, Mar. 2003.
43. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Parisi, "Defining and identifying communities in networks," Proc. Nat. Acad. Sci. USA, vol. 101, no. 9, pp. 2658-2663, Mar. 2004.
44. S. Asthana, O. D. King, F. D. Gibbons, and F. P. Roth, "Predicting protein complex membership using probabilistic network reliability," Genome Res., vol. 14, no. 6, pp. 1170-1175, Jun. 2004.
45. V. Batagelj and A. Mrvar, "Pajek: Program for large network analysis," Connections, vol. 21, pp. 47-57, 1998.
46. P. Y. Wu, C. Ruhlmann, F. Winston, and P. Schultz P, "Molecular architecture of the S. cerevisiae SAGA complex," Mol. Cell, vol. 15, no. 2, pp. 199-208, Jul. 2004.
47. B. Guglielmi, N. L. van Berkum, B. Klapholz, T. Bijma, M. Boube, C. Boschiero, H. M. Bourbon, F. C. P. Holstege, and M. Werner, "A high resolution protein interaction map ofthe yeast mediator complex," Nucl. Acids Res., vol. 32, no. 18, pp. 5379-5391, Oct. 2004.
48. J. Mendel, "Fuzzy logic systems for engineering: A tutorial," Proc. IEEE, vol. 83, no. 3, pp. 345-377, Mar. 1995.
49. B. A. Sokhansanj, J. B. Garnham, and J. P. Fitch, "Interpreting data from microarray experiments to build models of microbial genetic regulation networks," Proc. SPIE, vol. 4623, pp. 27-37, Jan. 2002.
50. B. A. Sokhansanj, G. R. Rodrigue, and J. P. Fitch JP, "Building and testing scalable fuzzy models of bacterial regulation," in Proc. 2002 Int. Conf. Comput. Nanosci. Nanotechnol., San Juan, Puerto Rico, Apr. 22-25, 2002.
51. B. A. Sokhansanj and D. M. Wilson 3rd, "Oxidative DNA damage background estimated by a system model of base excision repair," Free Rad. Biol. Med., vol. 37, no. 3, pp. 422-427, Aug. 2004.
52. W. E. Combs and J. E. Andrews, "Combinatorial rule explosion eliminated by a fuzzy rule configuration," IEEE Trans. Fuzzy Syst., vol. 6, pp. 1-11, Feb. 1998.
53. J. J. Weinschenk, R. J. Marks II, and W. E. Combs, "Layered URC fuzzy systems: A novel link between fuzzy systems and neural networks," in Proc. 2003 Int. Joint Conf. Neural Netw., Portland, OR, Jul. 20-24, 2003.
54. M. L. Whitfield, G. Sherlock, A. J. Saldanha, J. I. Murray, C. A. Ball, K. E. Alexander, J. C. Matese, C. M. Perou, M. M. Hurt, P. O. Brown, and D. Botstein, "Identification of genes periodically expressed in the human cell cycle and their expression in tumors," Mol. Biol. Cell. vol. 13, pp. 1977-2000, 2002.
55. K. Shedden and S. Cooper, "Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization," Proc. Nat. Acad. Sci. USA vol. 99, no. 7, pp. 4379-4384, Apr. 2002.