Identifying targets for intervention by analyzing basins of attraction

Pacific Symposium on Biocomputing 2011, PSB 2011

Volumn , Issue , 2011, Pages 350-361

  Verdicchio, Michael P ^a   Kim, Seungchan ^a,b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

Attractors; Boolean Networks; Intervention; Logic Minimization

Indexed keywords

ATTRACTORS; BASINS OF ATTRACTION; BOOLEAN NETWORK MODELS; BOOLEAN NETWORKS; CELLULAR PHENOTYPES; CIRCUIT DESIGNS; COMPLEX DYNAMICS; GENE EXPRESSION DATA; GRAND CHALLENGE; INDIRECT CONTROL; INTERVENTION; KEY VARIABLES; LOGIC MINIMIZATION; NETWORK MEASUREMENT; NETWORK MODELING; YEAST CELL CYCLES;

BOOLEAN ALGEBRA; DISEASES; GENE EXPRESSION; LOGIC CIRCUITS;

BIOLOGICAL SYSTEMS;

ONCOPROTEIN; WNT PROTEIN; WNT5A PROTEIN, HUMAN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CYTOLOGY; FUNGAL GENE; GENE; GENE REGULATORY NETWORK; GENETICS; HUMAN; MELANOMA; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE REGULATORY NETWORKS; GENES, CDC; GENES, FUNGAL; HUMANS; MELANOMA; MODELS, BIOLOGICAL; MODELS, GENETIC; PROTO-ONCOGENE PROTEINS; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; WNT PROTEINS;

EID: 84860450630     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (43)

1. J. Goutsias and S. Kim, Biophys J 86, 1922 (April 2004).
2. S. Kauffman, Journal of Theoretical Biology 22, 437 (March 1969).
3. G. Lima-Mendez and J. Helden, Mol. BioSyst. 5, 1482 (December 2009).
4. A. Wuensche, Genomic regulation modeled as a network with basins of attraction., in Pacific Symposium on Biocomputing, 1998.
5. F. Li, T. Long, Y. Lu, Q. Ouyang and C. Tang, Proceedings of the National Academy of Sciences of the United States of America 101, 4781 (April 2004).
6. R. Albert and H. G. Othmer, Journal of Theoretical Biology 223, 1 (July 2003).
7. J. Yu, V. A. Smith, P. P. Wang, A. J. Hartemink and E. D. Jarvis, Bioinformatics 20, bth448 (July 2004).
8. V. A. Smith, E. D. Jarvis and A. J. Hartemink, Bioinformatics 18, S216 (July 2002).
9. C. Gershenson, Classification of random boolean networks, in ICAL 2003: Proceedings of the eighth international conference on Artificial life, (MIT Press, Cambridge, MA, USA, 2003).
10. K. Klemm and S. Bornholdt, Physical Review E 72, 055101 (Nov 2005).
11. F. Greil and B. Drossel, Physical Review Letters 95, 048701 (Jul 2005).
12. X. Deng, H. Geng and M. Matache, Biosystems 88, 16 (March 2007).
13. T. Akutsu, S. Miyano and S. Kuhara, Pacific Symposium on Biocomputing, 17 (1999).
14. I. Shmulevich, A. Saarinen, O. Yli-Harja and J. Astola, Inference of genetic regulatory networks via best-fit extensions, in Computational and Statistical Approaches to Genomics, eds. W. Zhang and I. Shmulevich (Kluwer Academic Publishers, Boston, 2003) pp. 197-210.
15. H. L̈ahdesm̈aki, I. Shmulevich and O. Yli-Harja, Machine Learning 52, 147 (July 2003).
16. I. Shmulevich, E. R. Dougherty, S. Kim and W. Zhang, Bioinformatics 18, 261 (February 2002).
17. A. Datta, A. Choudhary, M. L. Bittner and E. R. Dougherty, Machine Learning 52, 169 (July 2003).
18. A. Datta, A. Choudhary, M. L. Bittner and E. R. Dougherty, Bioinformatics 20, 924 (April 2004).
19. R. Pal, A. Datta, M. L. Bittner and E. R. Dougherty, Bioinformatics 21, 1211 (April 2005).
20. A. Choudhary, A. Datta, M. L. Bittner and E. R. Dougherty, Bioinformatics 22, 226 (January 2006).
21. K. A. Richardson, Advances in Complex Systems 8, 365 (2005).
22. E. Dubrova, M. Teslenko and H. Tenhunen, A computational scheme based on random boolean networks, in Transactions on Computational Systems Biology X, eds. C. Priami, F. Dressler, O. B. Akan and A. Ngom, 2008) pp. 41-58.
23. J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger, Molecular Systems Biology 5 (December 2009).
24. R. Schlatter, K. Schmich, I. Avalos Vizcarra, P. Scheurich, T. Sauter, C. Borner, M. Ederer, I. Merfort and O. Sawodny, PLoS Comput Biol 5, e1000595 (December 2009).
25. L. J. Steggles, R. Banks, O. Shaw and A. Wipat, Bioinformatics 23, 336 (February 2007).
26. P. Maji, Fundam. Inf. 86, 143 (2008).
27. J. C. Mar and J. Quackenbush, PLoS Comput Biol 5, e1000626 (December 2009).
28. D. Bryce, M. P. Verdicchio and S. Kim, ACM Transactions on Intelligent Systems and Technology (To Appear).
29. M. P. Verdicchio and S. Kim, Reduction of Boolean Network Basins of Attraction Reveals Inter-vention Targets, tech. rep., Arizona State University (Tempe, AZ, 2010).
30. Y. Xiao, Current Genomics 10, 511 (November 2009).
31. I. Shmulevich, E. R. Dougherty and W. Zhang, Bioinformatics 18, 1319 (October 2002).
32. A. Marcovitz, Introduction to Logic Design, first edn. (McGraw-Hill, Feb 2002).
33. R. L. Rudell and A. L. Sangiovanni-Vincentelli, Espresso-mv: Algorithms for multiple valued logic minimization, in Proc. of the IEEE Custom Integrated Circuits Conference, 1985.
34. G. Scardoni, M. Petterlini and C. Laudanna, Bioinformatics 25, 2857 (November 2009).
35. I. Shmulevich and S. A. Kauffman, Physical Review Letters 93, 048701 (Jul 2004).
36. M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, A. Ben-Dor, N. Sampas, E. Dougherty, E.Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, J. Carpten, E. Gillanders, D. Leja, K. Dietrich, C. Beaudry, M. Berens, D. Alberts and V. Sondak, Nature 406, 536 (August 2000).
37. A. T. Weeraratna, Y. Jiang, G. Hostetter, K. Rosenblatt, P. Duray, M. Bittner and J. M. Trent, Cancer Cell 1, 279 (April 2002).
38. S. Kim, H. Li, E. R. Dougherty, N. Cao, Y. Chen, M. Bittner and E. B. Suh, Journal of Biological Systems 10, 337 (2002).
39. E. R. Dougherty, S. Kim and Y. Chen, Signal Processing 80, 2219 (2000).
40. S. Kim, E. R. Dougherty, M. L. Bittner, Y. Chen, K. Sivakumar, P. Meltzer and J. M. Trent, Journal of biomedical optics 5, 411 (October 2000).
41. J. Y. Y. Sung, S. M. M. Park, C.-H. H. Lee, J. W. W. Um, H. J. J. Lee, J. Kim, Y. J. Oh, S.-T. T. Lee, S. R. Paik and K. C. C. Chung, The Journal of biological chemistry 280, 25216 (July 2005).
42. A. Y. Law, K. P. Lai, C. K. Ip, A. S. Wong, G. F. Wagner and C. K. Wong, Experimental cell research 314, 1823 (May 2008).
43. S. Licciulli, C. Luise, A. Zanardi, L. Giorgetti, G. Viale, L. Lanfrancone, R. Carbone and M. Alcalay, BMC cell biology 11, 5 (January 2010).