Automatic modeling of signal pathways from protein-protein interaction networks

Series on Advances in Bioinformatics and Computational Biology

Volumn 6, Issue , 2008, Pages 287-296

  Zhao, Xing Ming ^a,b,c   Wang, Rui Sheng ^d   Chen, Luonan ^a,c,d   Aihara, Kazuyuki ^a,c  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b INSTITUTE OF INTELLIGENT MACHINES   (China)

^c INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^d OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC MODELING; INTEGER LINEAR PROGRAMMING MODELS; NUMERICAL RESULTS; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS; SIGNAL PATHWAYS; SIGNALING PATHWAYS; SUBNETWORKS;

ACTIVE NETWORKS; BIOINFORMATICS; COMPUTER PROGRAMMING; NUMERICAL METHODS;

PROTEINS;

EID: 84863116868     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (12)

1. Liu Y, Zhao H. A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics, 5: 158, 2004.
2. SteffenM, Petti A, Aach J, D'haeseleer P, Church G. Automated modelling of signal transduction networks. BMC Bioinformatics, 3:34, 2002.
3. Zien A, Kuffner R, Zimmer R, Lengauer T. Analysis of gene expression data with pathway scores. Proc Int Conf Intell Syst Mol Biol, 8:407-417, 2000.
4. Scott J, Ideker T, Karp RM, Sharan R. Efficient Algorithms for Detecting signaling pathways in Protein Interaction Networks. Journal of Computational Biology, 13: 133-144, 2006.
5. Bader, J., Chaudhuri, A., Rothberg, J., Chant, J. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnol, 22: 78-85, 2003.
6. Deng M, Sun F, Chen T. Assessment of the reliability of protein-protein in-teractions and protein function prediction. In: Proceedings of the Eighth Pacific Symposium on Biocomputing, 140-51, 2003
7. vonMering C, Krause R, Snel B, CornellM, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417:399-403, 2002. (Pubitemid 34563526)
8. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. PNAS, 102: 1974-1979, 2005. (Pubitemid 40261997)
9. Xenarios I, et al. DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30: 303-305, 2002 (Pubitemid 34679570)
10. Mewes HW, Amid C, et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Research, 32: Database issue:D41-4, 2004. (Pubitemid 38081600)
11. Wang L, Xu Y. Haplotype inference by maximum parsimony. Bioinformatics, 19,1773-1780, 2003. (Pubitemid 37220469)
12. Tobias H, Andor L, Robert F, Helgi B Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins. Biochim. Biophys. Acta, 1725, 19-29, 2005.