Multimodal networks: Structure and operations

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 6, Issue 2, 2009, Pages 321-332

  Heath, Lenwood S ^a   Sioson, Allan A ^b  

^a State University

^b Ateneo de Naga University   (Philippines)

Author keywords

Biological networks; Biot.; Graph; Hypergraph; Mode; Multimodal network

Indexed keywords

BIOLOGICAL NETWORKS; BIOT.; GRAPH; HYPERGRAPH; MODE; MULTIMODAL NETWORK;

DATABASE SYSTEMS;

GRAPH THEORY;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER LANGUAGE; DATA BASE; GENE REGULATORY NETWORK; GENETIC DATABASE; METABOLISM; METHODOLOGY; SIGNAL TRANSDUCTION;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE REGULATORY NETWORKS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PROGRAMMING LANGUAGES; SIGNAL TRANSDUCTION;

EID: 67549137262     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.70243     Document Type: Article

References (29)

1. I. Pirson, N. Fortemaison, C. Jacobs, S. Dremier, J.E. Dumont, and C. Maenhaut, "The Visual Display of Regulatory Information and Networks," Trends in Cell Biology, vol. 10, pp. 404-408, 2000.
2. K. Fukuda and T. Takagi, "Knowledge Representation of Signal Transduction Pathways," Bioinformatics, vol. 17, no. 9, pp. 829-837, 2001.
3. S. Xanthoudakis and D.W. Nicholson, "Heat-Shock Proteins as Death Determinants," Nature Cell Biology, vol. 2, pp. E163-E165, 2000.
4. P. Holme, M. Huss, and H. Jeong, "Subnetwork Hierarchies of Biochemical Pathways," Bioinformatics, vol. 19, no. 4, pp. 532-538, 2003.
5. S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch, and T. Dandekar, "Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae," Bioinformatics, vol. 18, no. 2, pp. 351-361, 2002.
6. H. Ma and A.-P. Zeng, "Reconstruction of Metabolic Networks from Genome Data and Analysis of Their Global Structure for Various Organisms," Bioinformatics, vol. 19, no. 2, pp. 270-277, 2003.
7. C.V. Forst, C. Flamm, I.L. Hofacker, and P.F. Stadler, "Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation," BMC Bioinformatics, vol. 7, no. 67, Feb. 2006.
8. L.S. Heath, "Networks in Bioinformatics," Proc. Int l Symp. Parallel Architectures, Algorithms, and Networks (I-SPAN '02), pp. 141-150, 2002.
9. A.A. Sioson and L.S. Heath, "Some Fundamental Operations on Multimodal Networks in Biology," Philippine Computing J., vol. 1, no. 2, pp. 13-22, Dec. 2006.
10. L.S. Heath and A.A. Sioson, "Semantics of Multimodal Network Models," IEEE/ACM Trans. Computational Biology and Bioinfor- matics, vol. 6, no. 2, pp. 271-280, Apr.-June 2009.
11. A.A. Sioson, "Multimodal Networks in Biology," Virginia Polytechnic Inst. and State Univ., Nov. 2005.
12. M. Stonebraker and G. Kemnitz, "The POSTGRES Next-Generation Database Management System," Comm. ACM, vol. 34, pp. 78-92, 1991.
13. M. Benjamins, C.D.R. Lindveld, and R. van Nes, "Multimodal Travel Choice Modeling Using a Supernetwork Approach," Proc. 81st Transportation Research Board Ann. Meeting, 2002.
14. K. Uchida, A. Sumalee, D. Watling, and R. Connors, "Study on Optimal Frequency Design Problem for Multimodal Network Using Probit-Based User Equilibrium Assignment," Transportation Research Board, no. 1923, pp. 236-245, 2005.
15. H. Abrach, S. Bhatti, J. Carlson, H. Dai, J. Rose, A. Sheth, B. Shuckler, J. Deng, and R. Han, "Mantis: System Support for Multimodal Networks of In-Situ Sensors," Proc. Second ACM Int l Workshop Wireless Sensor Networks and Applications (WSNA), 2003.
16. C. Berge, Hypergraphs. North-Holland, 1989.
17. G. Gallo, G. Longo, S. Pallottino, and S. Nguyen, "Directed Hypergraphs and Applications," Discrete Applied Math., vol. 42, pp. 177-201, 1993.
18. M.K. Campbell and S.O. Farrell, Biochemistry, fourth ed. Thomson Brooks/Cole, 2005.
19. W.H. Elliott and D.C. Elliott, Biochemistry and Molecular Biology. Oxford Univ. Press, 1997.
20. D.B. West, Introduction to Graph Theory, second ed. Prentice Hall, 2001.
21. B.C. Pierce, Basic Category Theory for Computer Scientists (Foundations of Computing). MIT Press, 1991.
22. Kyoto Encyclopedia of Genes and Genomes (KEGG) Website, http://www.kegg.org/, 2008.
23. J.-M. Bruey, C. Ducasse, P. Bonniaud, L. Ravagnan, S.A. Susin, C. Diaz-Latoud, S. Gurbuxani, A.-P. Arrigo, G. Kroemer, E. Solary, and C. Garrido, "HSP27 Negatively Regulates Cell Death by Interacting with Cytochrome c," Nature Cell Biology, vol. 2, pp. 645-652, 2000.
24. A. Saleh, S.M. Srinivasula, L. Balkir, and P.D. Robbins, "Negative Regulation of the APAF-1 Apoptosome by HSP70," Nature Cell Biology, vol. 2, pp. 476-483, 2000.
25. H.M. Beere, B.B. Wolf, K. Cain, D.D. Mosser, A. Mahboubi, T. Kuwana, P. Tailor, R.I. Morimoto, and G.M. Cohen, "Heat-Shock Protein 70 Inhibits Apoptosis by Preventing Recruitment of Procaspase-9 to the APAF-1 Apoptosome," Nature Cell Biology, vol. 2, pp. 469-475, 2000.
26. M. Kanehisa, S. Goto, S. Kawashima, and A. Nakaya, "The KEGG Databases at GenomeNet," Nucleic Acids Research, vol. 30, no. 1, pp. 42-46, 2002.
27. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, "The KEGG Resources for Deciphering the Genome," Nucleic Acids Research, vol. 32, pp. D277-D280, 2004.
28. R.G. Alscher, B.I. Chevone, L.S. Heath, and N. Ramakrishnan, "Expresso-A Problem Solving Environment for Bioinformatics: Finding Answers with Microarray Technology," Proc. High Performance Computing Symp, Advanced Simulation Technologies Conf. (HPC '01), pp. 64-69, 2001.
29. A.A. Sioson, J.I. Watkinson, C. Vasquez-Robinet, M. Ellis, M. Shukla, D. Kumar, N. Ramakrishnan, L.S. Heath, R. Grene, B.I. Chevone, K. Kadafar, and L.T. Watson, "Expresso and Chips: Creating a Next Generation Microarray Experiment Management System," Proc. Int'l Parallel and Distributed Processing Symp. Next Generation Software Systems Workshop (IPDPS '03), p. 209b, Apr. 2003.