Data mining and predictive modeling of biomolecular network from biomedical literature databases

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 4, Issue 2, 2007, Pages 251-263

  Hu, Xiaohua ^a   Wu, Daniel D ^a  

^a Drexel University   (United States)

Author keywords

Biological complexes (communities); Biomolecular network; Information extraction; Scale free network; Semisupervised learning

Indexed keywords

BIOLOGICAL COMPLEXES (COMMUNITIES); BIOMOLECULAR NETWORKS; INFORMATION EXTRACTION; SCALE FREE NETWORKS; SEMISUPERVISED LEARNING;

BIOINFORMATICS; CLUSTERING ALGORITHMS; DATABASE SYSTEMS; GENES; NEURAL NETWORKS; PROTEINS;

DATA MINING;

PROTEOME;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DATA BASE; EVALUATION; GENE EXPRESSION; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; PUBLICATION; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; GENE EXPRESSION; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; PERIODICALS; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION;

EID: 34248330400     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.070211     Document Type: Article

References (48)

1. S. Asthana, O.D. King, F.D. Gibbons, and P.P. Roth, "Predicting Protein Complex Membership Using Probabilistic Network Reliability," Genome Research, vol. 14, pp. 1170-1175, 2004.
2. G.D. Bader, I. Donaldson, C. Wolting, B.F. Quellette, T. Pawson, and C.W. Hogue, "BIND-The Biomolecular Interaction Network Database," Nucleic Acids Research, vol. 29, no. 1, pp. 242-245, 2001.
3. A.-L. Barabási and A. Reka, "Emergence of Scaling in Random Networks," Science, vol. 286, pp. 509-512, Oct. 1999.
4. V. Batagelj and A. Mrvar, "Pajek: Program for Large Network Analysis," Connections, vol. 21, pp. 47-57, 1998.
5. C. Blaschke, M.A. Andrade, C. Ouzounis, and A. Valencia, "Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions," Proc. Int'l Conf. Intelligent Systems in Molecular Biology, pp. 60-67, 1999.
6. A. Blum and T. Mitchell, "Combining Labeled and Unlabeled Data with Co-Training," Proc. 11th Ann, Conf. Computational Learning Theory, pp. 92-100, 1998.
7. S. Brin, "Extracting Patterns and Relations from the World Wide Web," Proc. 1998 Int'l Workshop Web and Databases (WebDB '98), pp. 172-183,1998.
8. B. Cestnik, "Estimating Probabilities: A Crucial Task in Machine Learning," Proc. Europe Conf. AI, 1990.
9. J.H. Chiang and H.H. Yu, "MeKE; Discovering the Functions of Gene Products from Biomédical Literature via Sentence Alignment," Bioinformatics, vol. 19, no. 11, pp. 1417-1422, 2003.
10. W. Cohen, "Fast Effective Rule Induction," Proc. Int'l Conf. Machine Learning (ICML '95), 1995.
11. B. de Brujin and J. Martin, "Literature Mining in Molecular Biology," Proc. EFMI Workshop Natural Language, pp. 1-5, 2002.
12. J. Ding, D. Berleant, D. Nettleton, and E. Wurtele, "Mining Medline: Abstracts, Sentences, or Phrases," Proc. Pacific Symp. Biocomputing (PSB '02), pp. 326-337, 2002.
13. L. Donetti and M.A. Munoz, "Detecting Network Communities: A New Systematic and Efficient Algorithm," J. Statistical Mechanics, P10012, 2004.
14. G.W. Flake, S.R. Lawrence, C.L. Giles, and P.M. Coetzee, "Self-Organization and Identification of Web Communities," Computer, vol. 35, pp. 66-71, 2002.
15. K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi, "Toward Information Extraction: Identifying Protein Names from Biological Papers," Proc. Pacific Symp. Biocomputing (PSB '98), pp. 707-718, 1998.
16. A.-C. Gavin et al., "Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes," Nature, vol. 415, pp. 141-147, 2002.
17. M. Gavin and M.E.J. Newman, "Community Structure in Social and Biological Networks," Proc, Nat'1 Academy of Sciences USA, vol. 99, pp. 7821-7826, 2002.
18. U. Hahn, M. Romacker, and S. Schulz, "Creating Knowledge Repositories from Biomedical Reports: The MedSYnDikate Text Mining System," Proc. Pacific Symp. Biocomputing (PSB '02), pp. 338-349, 2002.
19. T. Hasegawa, S. Sekine, and G. Ralph, "Discovering Relations among Named Entities from Large Corpora," Proc. Ann. Meeting Assoc. Computational Linguistics (ACL '04), 2004.
20. L.H. Hartwell, J.J. Hopfield, S. Leibler, and A.W. Murray, "From Molecular to Modular Cell Biology," Nature, vol. 402, pp. C47-C52, 1999.
21. R.F. Hashimoto, S. Kim, I. Shmulevich, W. Zhang, M.L. Bittner, and E.R. Dougherty, "Growing Genetic Regulatory Networks from Seed Genes," Bioinformatics, vol. 20, no. 8, pp. 1241-1247, 2004.
22. 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, 2002.
23. Y. Ho et al., "Systematic Identification of Protein Complexes in Saccharmyces Cerevisiae by Mass Spectrometry," 'Nature, vol. 415, pp. 180-183, 2002.
24. P. Holme, M. Huss, and H. Jeong, "Subnetwork Hierarchies of Biochemical Pathways," Bioinformatics, vol. 19, no. 4, pp. 532-538, 2003.
25. X. Hu and N. Cereone, "Discovering Maximal Generalized Decision Rules through Horizontal and Vertical Data Reduction," Computational Intelligence; An Int'l J., vol. 17, no. 4, pp. 685-702, 2001.
26. X. Hu, T.Y Lin, I.-Y. Song, X. Lin, I. Yoo, M. Lechner, and M. Song, "Ontology-Based Scalable and Portable Information Extraction System to Extract Biological Knowledge from Huge Collection of Biomedical Web Documents," Proc. IEEE/ACM Web Intelligence Conf., pp. 77-83, Sept. 2004.
27. X. Hu, I. Yoo, M. Song, J. Han, and M. Lechner, "Extracting and Mining Protein-Protein Interaction Network from Biomedical Literature," Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB '04), Oct. 2004.
28. X. Hu, "Mining and Analyzing Scale-Free Protein-Protein Interaction Network," Int'l J. Bioinformatics Research and Application, vol. 1, no. 1, pp. 81-101, 2005.
29. R. Jansen, N. Lan, J. Qian, and M. Gerstein, "Integration of Genomic Datasets to Predict Protein Complexes in Yeast," J. Structural Functional Genomics, vol. 2, pp. 71-81, 2002.
30. M. Kanehisa and S. Goto, "A Systematic Analysis of Gene Functions by the Metabolic Pathway Database," Theoretical and Computational Methods in Genome Research, S. Suhai, ed., pp. 41-55, Plenum Press, 1997.
31. J. Kleinberg, "Authoritative Sources in a Hyperlinked Environment," Proc. Ninth ACM-SIAM Symp. Discrete Algorithms, 1998.
32. B. Liu, W. Hsu, and Y. Ma, "Integrating Classification and Association Rule Mining," Proc. Int'l Conf. Knowledge Discovery and Dataming (KDD '98), 1998.
33. E.M. Marcott, I. Xenarios, and D. Eisenberg, "Mining Literature for Protein-Protein Interactions," Bioinformatics, vol. 17, no. 4, pp. 359-363, 2001.
34. M.E.J. Newman, "The Structure and Function of Complex Networks," SIAM Rev., vol. 45, no. 2, pp. 167-256, 2003.
35. M.E.J. Newman, "Detecting Community Structure in Networks," European Physics J. B, vol. 38, pp. 321-330, 2004.
36. 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, 2001.
37. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Parisi, "Defining and Identifying Communities in Networks," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 2658-2663, 2004.
38. E. Riloff, "Automatically Generating Extraction Patterns from Untagged Text," Proc. 13th Nat'l Conf. Artificial Intelligenc (AAAI '96), pp. 1044-1049, 1996.
39. S. Soderland, "Learning Information Extraction Rules for Semi-Structured and Free Text," Machine Learning, vol. 34, pp. 233-272, 1999.
40. V. Spirin and L.A. Mirny, "Protein Complexes and Functional Modules in Molecular Networks," Proc. Nat'l Academy Sciences USA, vol. 100, pp. 12123-12128, 2003.
41. B.J. Stapley and G. Benoit, "Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts," Proc. Pacific Symp. Biocomputing (PSB '00), pp. 529-540, 2000.
42. V. Vapnik, The Nature of Statistical Learning Theory. Springer-Verlag, 1995.
43. J. Weizenbaum, "ELIZA - A Computer Program for the Study of Natural Language Communications between Men and Machine," Comm. ACM, vol. 9, pp. 36-45, 1966.
44. S. White and P. Smyth, "A Spectral Clustering Approach to Finding Communities in Graphs," Proc. SIAM Int'l Conf. Data Mining, 2005.
45. D. Wilkinson and B.A. Huberman, "A Method for Finding Communities of Related Genes," Proc. Nat'1 Academy of Sciences USA, vol. 101, supplement 1, pp. 5241-5248, 2004.
46. D. Wu and X. Hu, "An Efficient Approach to Detecting a Protein Community from a Seed," Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology, 2005.
47. I. Xenarios, E. Fernandez, L. Salwinski, X.J. Duan, M.J. Thompson, E.M. Marcotte, and D. Eisenberg, "DIP: The Database of Interacting Proteins: 2001 Update," Nucleic Acids Reg., vol. 29, pp. 239-241, 2001.
48. D. Zelenko, C. Aone, and A. Richardella, "Kernel Methods for Relation Extraction," J. Machine Learning Research, vol. 3, pp. 1083-1106, 2003.