Discovery of a kernel for controlling biomolecular regulatory networks

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Kim, Junil ^a   Park, Sang Min ^a   Cho, Kwang Hyun ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DRUG DEVELOPMENT; DRUG EFFECT; GENE REGULATORY NETWORK; HUMAN; MOUSE; PHENOTYPE; PLANT; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; DRUG EFFECTS;

ANIMALS; COMPUTER SIMULATION; DRUG DISCOVERY; GENE REGULATORY NETWORKS; HUMANS; MICE; MODELS, BIOLOGICAL; PHENOTYPE; PLANTS; PROTEIN BINDING; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION;

PROTEIN BINDING;

EID: 84880347253     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02223     Document Type: Article

References (36)

1. Kim, J. et al. Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity. Bioinformatics 24, 1516-1522 (2008). (Pubitemid 351911703)
2. Kim, J. R. et al. Reduction of complex signaling networks to a representative kernel. Sci Signal 4, ra35 (2011).
3. Kim, T. H., Kim, J., Heslop-Harrison, P. & Cho, K. H. Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. Bioinformatics 27, 245-251 (2011).
4. Choi, M., Shi, J., Jung, S. H., Chen, X. & Cho, K.-H. Attractor landscape analysis reveals feedback loops in the p53 network that control the cellular response to DNA damage. Science Signaling 5, ra83 (2012).
5. Ding, S. , Wang, W. Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. BMC Syst Biol 5, 50 (2011).
6. Huang, S., Eichler, G., Bar-Yam, Y. & Ingber, D. E. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 94, 128701 (2005).
7. Li, F., Long, T., Lu, Y., Ouyang, Q. & Tang, C. The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101, 4781-4786 (2004). (Pubitemid 38469154)
8. Wang, G. et al. Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci USA 107, 10478-10483 (2010).
9. Liu, Y. Y., Slotine, J. J. & Barabasi, A. L. Controllability of complex networks. Nature 473, 167-173 (2011).
10. Nepusz, T. & Vicsek, T. Controlling edge dynamics in complex networks. Nat Phys 8, 568-573 (2012).
11. Liu, Y. Y., Slotine, J. J. & Barabasi, A. L. Control centrality and hierarchical structure in complex networks. PLoS One 7, e44459 (2012).
12. Helikar, T., Konvalina, J., Heidel, J. & Rogers, J. A. Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci USA 105, 1913-1918 (2008). (Pubitemid 351439439)
13. Saez-Rodriguez, J. et al. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol 5, 331 (2009).
14. Macarthur, B. D.,Ma'ayan, A. & Lemischka, I. R. Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol 10, 672-681 (2009).
15. Chen, L., Liu, R., Liu, Z. P., Li, M. & Aihara, K. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci Rep 2, 342 (2012).
16. Shin, S. Y. et al. Functional roles of multiple feedback loops in extracellular signalregulated kinase and Wnt signaling pathways that regulate epithelialmesenchymal transition. Cancer Res 70, 6715-6724 (2010).
17. Giacomantonio, C. E. & Goodhill, G. J. A Boolean model of the gene regulatory network underlying Mammalian cortical area development. PLoS Comput Biol 6 (2010).
18. Alvarez-Buylla, E. R. et al. Gene regulatory network models for plant development. Curr Opin Plant Biol 10, 83-91 (2007). (Pubitemid 46098929)
19. Krumsiek, J., Marr, C., Schroeder, T. & Theis, F. J. Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS One 6, e22649 (2011).
20. Sahin, O. et al. Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol 3, 1 (2009).
21. Abdi, A., Tahoori, M. B. & Emamian, E. S. Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways. Sci Signal 1, ra10 (2008).
22. Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J., 3rd & Doyle, J. Robustness of cellular functions. Cell 118, 675-685 (2004). (Pubitemid 39221728)
23. Assenov, Y., Ramirez, F., Schelhorn, S. E., Lengauer, T. & Albrecht, M. Computing topological parameters of biological networks. Bioinformatics 24, 282-284 (2008).
24. Dong, J. & Horvath, S. Understanding network concepts in modules. BMC Syst Biol 1, 24 (2007).
25. Liu, Y. Y., Slotine, J. J. & Barabasi, A. L. Observability of complex systems. Proc Natl Acad Sci USA 110, 2460-2465 (2013).
26. Kauffman, S., Peterson, C., Samuelsson, B. & Troein, C. Genetic networks with canalyzing Boolean rules are always stable. Proc Natl Acad Sci USA 101, 17102-17107 (2004). (Pubitemid 39627781)
27. Huang, S. Reprogramming cell fates: reconciling rarity with robustness. Bioessays 31, 546-560 (2009).
28. Kauffman, S., Peterson, C., Samuelsson, B. , Troein, C. Random Boolean network models and the yeast transcriptional network. Proc Natl Acad Sci USA 100, 14796-14799 (2003). (Pubitemid 37517970)
29. Aldridge, B. B., Burke, J. M., Lauffenburger, D. A. & Sorger, P. K. Physicochemical modelling of cell signalling pathways. Nat Cell Biol 8, 1195-1203 (2006). (Pubitemid 44660581)
30. Muller, F. J. & Schuppert, A. Few inputs can reprogram biological networks. Nature 478, E4; discussion E4-5 (2011).
31. Ieda, M. et al.Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375-386 (2010).
32. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676 (2006). (Pubitemid 44233629)
33. Zhou, J. X. & Huang, S. Understanding gene circuits at cell-fate branch points for rational cell reprogramming. Trends Genet 27, 55-62 (2011).
34. Beasley, D., Bull, D. R. & Martin, R. R. An Overview of Genetic Algorithms.1. Fundamentals. U Comput 15, 58-69 (1993).
35. Wishart, D. S. et al. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36, D901-906 (2008). (Pubitemid 351149842)
36. Kuhn, M., von Mering, C., Campillos, M., Jensen, L. J. & Bork, P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36, D684-688 (2008). (Pubitemid 351149807)