Detecting functional modules from protein interaction networks

First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06

Volumn 1, Issue , 2006, Pages 123-130

  Luo, Feng ^a   Scheuermann, Richard H ^b  

^a Clemson University   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; GENES; GRAPH THEORY; STATISTICAL METHODS; YEAST;

BIOLOGICAL SYSTEMS; FUNCTIONAL MODULES; GENE ONTOLOGY; YEAST CORE PROTEINS;

PROTEINS;

EID: 33845587939     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IMSCCS.2006.55     Document Type: Conference Paper

References (24)

1. V. Arnau, S. Mars, I. Marin, 'Iterative Cluster Analysis of Protein Interaction Data," Bioinformatics, 21, 3, pp. 364-378, 2005.
2. G. D. Bader, C. W. V. Hogue, "An automated method for finding molecular complexes in large protein interaction networks," BMC Bioinformatics, 4:2, 2003.
3. R. Balakrishnan, et al., Saccharomyces Genome Database, http://www.yeastgenome.org/ftp://ftp.yeastgenome.org/yeast/
4. A.-L. Barabasi, Z. N. Oltvai, "Network Biology: Understanding the cell's functional organization," Nature Review, 5, pp. 101-114, 2004.
5. D. Bu, Y. Zhao, L. Cai, H. Xue, X. Zhu, H. Lu, J. Zhang, S. Sun, L. Ling, N. Zhang, G. Li, R. Chen, "Topological structure analysis of the protein-protein interaction network in budding yeast," Nucleic Acids Research, 31, pp. 2443-2450, 2003.
6. J. M. Cherry, C. Adler, C. Ball, S. A. Chervitz, S. S. Dwight, E. T. Hester, Y. Jia, G. Juvik, T. Roe, M. Schroeder, S. Weng, D. Botstein, "SGD: Saccharomyces Genome Database," Nucleic Acids Research, 26, 1, pp. 73-79, 1998.
7. C. M. Deane, L. Salwinski, I. Xenarios, D. Eisenberg, "Protein interactions: Two methods for assessment of the reliability of high-throughput observations," Molecular & Cellular Proteomics, 1, pp. 349-356, 2002.
8. A. J. Enright, C. A. Ouzounis, "BioLayout - an automatic graph layoutalgorithm for similarity visualization," Bioinformatics, 17, pp. 853-854, 2001.
9. J. Gagneur, R. Krause, T. Bouwmeester, G. Casari, "Modular decomposition of protein-protein interaction networks," Genome Biology, 5, R57, 2004.
10. M. Girvan, M. E. J. Newman, "Community structure in social and biological networks," PNAS, 99, 12, pp. 7821-7826, 2002.
11. L. H. Hartwell, J. J. Hopfiled, S. Leibler, A. W. Murray, "From Molecular to modular cell biology," Nature, 402, pp. C47-C52, 1999.
12. J. MacCuish, C. Nicolaou, N. E. MacCuish, "Ties in proximity and clustering compounds," Journal of Chemical Information & Computer Sciences, 41, pp. 134-146, 2001.
13. M. E. J. Newman, "Fast algorithm for detecting community structure in networks," Physical Review E, 69, 066133, 2004.
14. M. E. J. Newman and M. Girvan, "Finding and evaluating community structure in networks," Physical Review E, 69, 026113, 2004.
15. J. B. Pereira-Leal, A. J. Enright, C. A. Ouzounis, "Detection of Functional Modules from Protein Interaction Networks," Proteins: Structure, Function, and Bioinformatics, 54, pp. 49-57, 2004.
16. N. Przulj, D. A. Wigle, I. Jurisica, "Functional topology in a network of protein interactions," Bioinformatics, 20, 340-348, 2004.
17. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, D. Parisi, "Defining and identifying communities in networks," PNAS, 101, 9, 2658-2663, 2004.
18. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, A.-L. Barabási, "Hierarchical Organization of Modularity in Metabolic Networks," Science, 297, 1551-1555, 2002.
19. A. W. River, T. Galitski, "Modular organization of cellular networks," PNAS, 100, 3, 1128-1133, 2003.
20. B. Snel, P. Bork, M. A. Huynen, "The identification of functional modules from the genomic association of genes," PNAS, 99, 5890-5895, 2002.
21. V. Spirin, L. A. Mirny, "Protein complexes and functional modules in molecular networks," PNAS 100, 12123-12128, 2003.
22. S. Wasserman, K. Faust, Social Network Analysis. Cambridge Univ. Press, Cambridge, U.K, 1994.
23. T. Wilhelm, H.-P. Nasheuer, S. Huang, "Physical and Functional Modularity of the Protein Network in Yeast," Molecular & Cellular Proteomics, 2, pp. 292-298, 2003.
24. I. Xenarios, L. Salwínski, X. Q. Duan, P. Higney, S. M. Kim, D. Eisenberg, "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions," Nucleic Acids Research, 30, 1, pp. 303-305, 2002.