Strategies for network motifs discovery

e-Science 2009 - 5th IEEE International Conference on e-Science

Volumn , Issue , 2009, Pages 80-87

  Ribeiro, Pedro ^a   Silva, Fernando ^a   Kaiser, Marcus ^b,c  

^a UNIVERSITY OF PORTO   (Portugal)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c Seoul National University   (South Korea)

Author keywords

Algorithms; Complex networks; Graph mining; Network motifs

Indexed keywords

COMMON PLATFORM; COMPLEX NETWORKS; DETECTION ALGORITHM; E-SCIENCE; GRAPH ISOMORPHISM; GRAPH MINING; NETWORK MOTIF; PSEUDO-CODE; RUNTIMES; SUBGRAPH MINING;

BIOLOGY; SET THEORY;

ALGORITHMS;

EID: 77949856178     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/e-Science.2009.20     Document Type: Conference Paper

References (42)

1. R. Albert and A. L. Barabasi, "Statistical mechanics of complex networks," Reviews of Modern Physics, vol. 74, no. 1, 2002.
2. S. N. Dorogovtsev and J. F. F. Mendes, "Evolution of networks," Advances in Physics, vol. 51, no. 4, pp. 1079-1187, June 2002.
3. M. E. J. Newman, "The structure and function of complex networks," SIAM Review, vol. 45, 2003.
4. S. Boccaletti, V. Latora, Y. Moreno, M. Chavez, and D. Hwang, "Complex networks: Structure and dynamics," Physics Reports, vol. 424, no. 4-5, pp. 175-308, February 2006.
5. M. Kaiser, "Brain architecture: a design for natural computation," Philos Transact A Math Phys Eng Sci, vol. 365, pp. 3033-3045, December 2007.
6. E. Ziv, R. Koytcheff, M. Middendorf, and C. Wiggins, "Systematic identification of statistically significant network measures," Physical Review E, vol. 71, p. 016110, 2005.
7. D. Chakrabarti and C. Faloutsos, "Graph mining: Laws, generators, and algorithms," ACM Computing Surveys, vol. 38, p. 1, 2006.
8. L. da F. Costa, F. A. Rodrigues, G. Travieso, and P. R. V. Boas, "Characterization of complex networks: A survey of measurements," Advances In Phyiscs, vol. 56, p. 167, 2007.
9. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, "Network motifs: simple building blocks of complex networks." Science, vol. 298, no. 5594, pp. 824-827, October 2002.
10. M. Kuramochi and G. Karypis, "Frequent subgraph discovery," IEEE International Conference on Data Mining, vol. 0, p. 313, 2001.
11. J. Han and M. Kamber, Data Mining, Second Edition: Concepts and Techniques. Morgan Kaufmann, September 2006.
12. R. Agrawal and R. Srikant, "Fast algorithms for mining association rules," in Proc. 20th Int. Conf. Very Large Data Bases, VLDB, 1994, pp. 487-499.
13. I. Albert and R. Albert, "Conserved network motifs allow protein-protein interaction prediction." Bioinformatics, vol. 20, no. 18, pp. 3346-3352, December 2004.
14. S. S. Shen-Orr, R. Milo, S. Mangan, and U. Alon, "Network motifs in the transcriptional regulation network of escherichia coli," Nature Genetics, vol. 31, no. 1, pp. 64-68, May 2002.
15. R. Dobrin, Q. K. Beg, A. Barabasi, and Z. Oltvai, "Aggregation of topological motifs in the escherichia coli transcriptional regulatory network," BMC Bioinformatics, vol. 5, p. 10, 2004.
16. M. Kondoh, "Building trophic modules into a persistent food web," Proceedings of the National Academy of Sciences, vol. 105, no. 43, pp. 16 631-16 635, 2008.
17. O. Sporns and R. Kotter, "Motifs in brain networks," PLoS Biology, vol. 2, 2004.
18. S. Itzkovitz, R. Levitt, N. Kashtan, R. Milo, M. Itzkovitz, and U. Alon, "Coarse-graining and self-dissimilarity of complex networks." Physical Review E, vol. 71, no. 1 Pt 2, January 2005.
19. S. Valverde and R. V. Solé, "Network motifs in computational graphs: A case study in software architecture," Physical Review E, vol. 72, no. 2, 2005.
20. A. Vazquez, R. Dobrin, D. Sergi, J. P. Eckmann, Z. N. Oltvai, and A. L. Barabasi, "The topological relationship between the large-scale attributes and local interaction patterns of complex networks," Proceedings of the National Academy of Sciences, vol. 101, p. 17945, 2004.
21. J. Hallinan and P. Jackway, "Network motifs, feedback loops and the dynamics of genetic regulatory networks," in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005.
22. P. J. Ingram, M. P. Stumpf, and J. Stark, "Network motifs: structure does not determine function," BMC Genomics, vol. 7, p. 108, 2006.
23. B. McKay, "Practical graph isomorphism," Congressus Numerantium, vol. 30, pp. 45-87, 1981.
24. G. Ciriello and C. Guerra, "A review on models and algorithms for motif discovery in protein-protein interaction networks," Briefings in Functional Genomics and Proteomics, vol. 7, no. 2, pp. 147-156, 2008.
25. D. S. Callaway, J. E. Hopcroft, J. M. Kleinberg, M. E. J. Newman, and S. H. Strogatz, "Are randomly grown graphs really random?" Physical Review E, vol. 64, no. 4, p. 041902, September 2001.
26. R. Milo, S. Itzkovitz, N. Kashtan, R. Levitt, S. Shen-Orr, I. Ayzenshtat, M. Sheffer, and U. Alon, "Superfamilies of evolved and designed networks." Science, vol. 303, no. 5663, pp. 1538-1542, March 2004.
27. V. Lacroix, C. G. Fernandes, and M. F. Sagot, "Motif search in graphs: Application to metabolic networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 360-368, Oct.-Dec. 2006.
28. M. Fellows, G. Fertin, D. Hermelin, and S. Vialette, "Sharp tractability borderlines for finding connected motifs in vertex-colored graphs," in In Proc. 34th Int. Colloquium on Automata, Languages and Programming (ICALP), 2007.
29. M. Middendorf, E. Ziv, and C. H. Wiggins, "Inferring network mechanisms: the drosophila melanogaster protein interaction network." Proceedings of the National Academy of Sciences, vol. 102, no. 9, pp. 3192-3197, March 2005.
30. J. Chen, W. Hsu, M. L. Lee, and S.-K. Ng, "Nemofinder: dissecting genome-wide protein-protein interactions with meso-scale network motifs," in Proc. of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. New York, NY, USA: ACM, 2006, pp. 106-115.
31. L. Parida, "Discovering topological motifs using a compact notation," Journal of Computational Biology, vol. 14, no. 3, pp. 300-323, 2007.
32. F. Schreiber and H. Schwobbermeyer, "Towards motif detection in networks: Frequency concepts and flexible search," in Proc. of the Int. Workshop on Network Tools and Applications in Biology (NETTAB04), 2004, pp. 91-102.
33. N. Kashtan, S. Itzkovitz, R. Milo, and U. Alon, "Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs," Bioinformatics, vol. 20, no. 11, pp. 1746-1758, 2004.
34. C. Matias, S. Schbath, E. Birmel, J.-J. Daudin, and S. Robin, "Network motifs: mean and variance for the count," REVSTAT, vol. 4, pp. 31-35, 2006.
35. S. Wernicke, "Efficient detection of network motifs," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 347-359, 2006.
36. F. Picard, J.-J. J. Daudin, M. Koskas, S. Schbath, and S. Robin, "Assessing the exceptionality of network motifs." Journal of Computational Biology, February 2008.
37. S. Schbath, V. Lacroix, and M. Sagot, "Assessing the exceptionality of coloured motifs in networks," EURASIP J. on Bioinformatics and Systems Biology, 2008.
38. S. Wernicke and F. Rasche, "Fanmod: a tool for fast network motif detection," Bioinformatics, vol. 22, no. 9, pp. 1152-1153, May 2006.
39. J. Grochow and M. Kellis, "Network motif discovery using subgraph enumeration and symmetry-breaking," Research in Computational Molecular Biology, pp. 92-106, 2007.
40. B. McKay, "Isomorph-free exhaustive generation," Journal of Algorithms, vol. 26, no. 2, pp. 306-324, 1998.
41. M. E. J. Newman, S. H. Strogatz, and D. J. Watts, "Random graphs with arbitrary degree distributions and their applications," Physical Review E, vol. 64, no. 2, p. 026118, July 2001.
42. A. Lancichinetti, S. Fortunato, and F. Radicchi, "Benchmark graphs for testing community detection algorithms," Physical Review E, vol. 78, no. 4, 2008.