Specification and simulation of synthetic multicelled behaviors

ACS Synthetic Biology

Volumn 1, Issue 8, 2012, Pages 365-374

  Jang, Seunghee S ^a   Oishi, Kevin T ^a   Egbert, Robert G ^a   Klavins, Eric ^a  

^a University of Washington   (United States)

Author keywords

Bacterial growth; Multicelled behavior; Pattern formation; Specification

Indexed keywords

ARTICLE; BACTERIAL GROWTH; CELL DIVISION; CELL FUNCTION; CROWDING; ESCHERICHIA COLI; GRO; MORPHOGENESIS; NONHUMAN; PRIORITY JOURNAL; PROCEDURES; SIMULATION;

ALGORITHMS; COMPUTER SIMULATION; ESCHERICHIA COLI; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SOFTWARE; SYNTHETIC BIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 84868233914     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300034m     Document Type: Article

References (41)

1. Danino, T., Mondragon-Palomino1, O., Tsimring, L., and Hasty, J. (2010) Nature 463, 326-330.
2. Tamsir, A., Tabor, J., and Voigt, C. (2011) Nature 469, 212-215.
3. Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellen, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., and Sole, R. (2011) Nature 469, 207-211.
4. Basu, S., Gerchman, Y., Collins, C., Arnold, F., and Weiss, R. (2005) Nature 434, 1130-1134.
5. Sohka, T., Heins, R., Phelan, R., Greisler, J., Townsend, C., and Ostermeier, M. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 10135-10140.
6. Liu, C., Fu, X., Liu, L., Ren, X., Chau, C., Li, S., Xiang, L., Zeng, H., Chen, G., Tang, L., Lenz, P., Cui, X., Huang, W., Hwa, T., and Huang1, J. (2011) Science 334, 238-241.
7. You, L., Cox, R., Weiss, R., and Arnold, F. (2004) Nature 428, 868-871.
8. Tabor, J., Salis, H., Simpson, Z., Chevalier, A., Levskaya, A., Marcotte, E., Voigt, C., and AD, A. E. (2009) Cell 137, 1272-1281.
9. Waters, C., and Bassler, B. (2005) Annu. Rev. Cell Dev. Biol. 21, 319-346.
10. Bashor, C., Horwitz, A., Peisajovich, S., and WA, W. L. (2010) Annu. Rev. Biophys. 9, 515-537.
11. Chandran, D., Bergmann, F., and Sauro, H. (2009) J. Biol. Eng. 3, 19.
12. Myers, C., Barker, N., Jones, K., Kuwahara, H., Madsen, C., and Nguyen, N. (2009) Bioinformatics 1, 2848-2849.
13. Hucka, M., et al. (2003) Bioinformatics 9, 524-531.
14. Angermann, B. R., Klauschen, F., Garcia, A. D., Prustel, T., Zhang, F., Germain, R. N., and Meier-Schellersheim, M. (2012) Nat. Methods 9, 283-289.
15. Mogilner, A., and Odde, D. (2011) Trends Cell Biol. 21, 692-700.
16. Montagna, S., and Viroli, M. (2010) Electron. Notes Theor. Comput. Sci. 268, 115-129.
17. Affolter, M., Zeller, R., and Caussinus, E. (2009) Nat. Rev. Mol. Cell Biol. 10, 831-842.
18. Dupuy, L., Mackenzie, J., Rudge, T., and Haseloff, J. (2007) Ann. Botany 101, 1255-1265.
19. Kondo, S., and Miura, T. (2010) Science 329, 1616-1620.
20. Lynch, N. (1996) Distributed Algorithms, Morgan Kaufmann, San Francisco.
21. Michael, N., Fink, J., and Kumar, V. (2011) Autonomous Robots 30, 73-86.
22. Klavins, E. (2007) Control Syst. Mag. 24, 43-56.
23. Chandy, K. M., and Misra, J. (1988) Parallel Program Design: A Foundation, Addision-Wesley Reading, MA.
24. Fischer, M. J., Lynch, N. A., and Paterson, M. S. (1985) J. ACM 32, 374-382.
25. Klavins, E. (2004) in Algorithmic Foundations of Robotics V (Boissonnat, J.-D., Burdick, J., Goldberg, K., and Hutchinson, S., Eds.) Vol. 7, pp 275-292, Springer, Berlin/Heidelberg.
26. Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., T.F. Knight, J., Nagpal, R., Rauch, E., Sussman, G., and Weiss, R. (2000) Commun. ACM 43, 74-82.
27. Young, J., Locke, J., Altinok, A., Rosenfeld, N., Bacarian, T., Swain, S., Mjolsness, E., and Elowitz, M. (2012) Nat. Protoc. 7, 80-88.
28. Chipmunk 2 Physics Library. http://chipmunk-physics.net/.
29. Dijkstra, E. W. (1975) SIGPLAN Not. 10, 2-2.13.
30. Klavins, E., and Murray, R. M. (2004) IEEE Pervasive Comput. 3, 56-65.
31. Gillespie, D. T. (1977) J. Phys. Chem. 81, 2340-2361.
32. Huh, D., and Paulsson, J. (2011) Proc. Acad. Natl. Sci. U.S.A. 108, 15004-15009.
33. Mettetal, J., Muzzey, D., Pedraza, J., Ozbudak, E., and van Oudenaarden, A. (2006) Proc. Acad. Natl. Sci. U.S.A. 103, 7304-7309.
34. Alur, R., and Dill, D. L. (1994) Theor. Comput. Sci. 126, 183-235.
35. Lindner, A., Madden, R., Demarez, A., Stewart, E., and Taddei, F. (2008) Proc. Acad. Natl. Sci. U.S.A. 105, 3076-3081.
36. Christen, M., Kulasekara, H., Christen, B., Kulasekara, B., Hoffman, L., and Miller, S. (2010) Science 328, 1295-1297.
37. Mettetal, J. T., Muzzey, D., Gomez-Uribe, C., and van Oudenaarden, A. (2008) Science 319, 482-484.
38. Lu, T., Ferry, M., Weiss, R., and Hasty, J. (2008) Phys. Biol. 5, 036006.
39. Kampf, M. M., Engesser, R., Busacker, M., Horner, M., Karlsson, M., Zurbriggen, M. D., Fussenegger, M., Timmer, J., and Weber, W. Mol. BioSyst. 8, 1824-1832.
40. Gardner, T., Cantor, C., and Collins, J. (2000) Nature 403, 339-342.
41. Bonnet, J., Subsoontorn, P., and Endy, D. (2012) Proc. Acad. Natl. Sci. U.S.A. 109, 8884-8889.