What can formal methods bring to systems biology?

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5850 LNCS, Issue , 2009, Pages 16-22

  Bonzanni, Nicola ^a   Feenstra, K Anton ^a   Fokkink, Wan ^a   Krepska, Elzbieta ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ELEGANS; POSITION PAPERS; SYSTEMS BIOLOGY;

BIOLOGY; PETRI NETS;

FORMAL METHODS;

EID: 70649106320     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-05089-3_2     Document Type: Conference Paper

References (22)

1. Barnat, J., Brim, L., Cerná, I., Drazan, S., Safránek, D.: Parallel model checking large-scale genetic regulatory networks with DiVinE. In: Proc. FBTC 2007. ENTCS, vol. 194(3), pp. 35-50. Elsevier, Amsterdam (2008)
2. Bonzanni, N., Krepska, E., Feenstra, A., Fokkink, W., Kielmann, T., Bal, H., Heringa, J.: Executing multicellular differentiation: Quantitative predictive modelling of C. elegans vulval development. Bioinformatics (in press)
3. Burkhard, H.-D.: On priorities of parallelism. In: Salwicki, A. (ed.) Logic of Programs 1980. LNCS, vol. 148, pp. 86-97. Springer, Heidelberg (1983)
4. Dobzhansky, T.: Nothing in Biology Makes Sense Except in the Light of Evolution. American Biology Teacher 35, 125-129 (1973)
5. Crombach, A., Hogeweg, P.: Evolution of evolvability in gene regulatory networks. PLoS Comput. Biol. 4, e1000112 (2008), doi:10.1371/journal.pcbi. 1000112
6. Fisher, J., Henzinger, T.: Executable cell biology. Nature Biotechnology 25(11), 1239-1249 (2007)
7. Fisher, J., Henzinger, T., Mateescu, M., Piterman, N.: Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol. 5054, pp. 17-32. Springer, Heidelberg (2008)
8. Fisher, J., Piterman, N., Hajnal, A., Henzinger, T.A.: Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Comput. Biol. 3, e92 (2007)
9. Fisher, J., Piterman, N., Jane Albert Hubbard, E., Stern, M.J., Harel, D.: Computational insights into Caenorhabditis elegans vulval development. P. Natl. Acad. Sci. USA 102, 1951-1956 (2005)
10. Giurumescu, C.A., Sternberg, P.W., Asthagiri, A.R.: Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development. P. Natl. Acad. Sci. USA 103, 1331-1336 (2006)
11. Harel, D.: A grand challenge for computing: Towards full reactive modeling of a multi-cellular animal. Bulletin of the EATCS 81, 226-235 (2003)
12. Kam, N., Harel, D., Kugler, H., Marelly, R., Pnueli, A., Jane Albert Hubbard, E., Stern, M.: Formal modeling of C. elegans development: A scenario-based approach. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 4-20. Springer, Heidelberg (2003)
13. Krepska, E., Bonzanni, N., Feenstra, A., Fokkink, W., Kielmann, T., Bal, H., Heringa, J.: Design issues for qualitative modelling of biological cells with Petri nets. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol. 5054, pp. 48-62. Springer, Heidelberg (2008)
14. Li, C., Nagasaki, M., Ueno, K., Miyano, S.: Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst. Biol. 3, 42 (2009)
15. Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.: Using Cell Illustrator and Pathway Databases. Springer, Heidelberg (2009)
16. Regev, A., Panina, E., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An abstraction for biological compartments. Theoretical Computer Science 325(1), 141-167 (2004)
17. Regev, A., Shapiro, E.: Cellular abstractions: Cells as computation. Nature 419, 343 (2002)
18. Sadot, A., Fisher, J., Barak, D., Admanit, Y., Stern, M., Hubbard, J.A., Harel, D.: Toward verified biological models. IEEE/ACM Transactions on Computational Biology and Bioin-formatics 5(2), 223-234 (2008)
19. Sternberg, P.W.: Chapter on vulval development in Wormbook (June 2005), http://www.wormbook.org/chapters/www-vulvaldev/vulvaldev.html
20. Sun, X., Hong, P.: Computational modeling of Caenorhabditis elegans vulval induction. Bioinformatics 507, i499-i507 (2007)
21. Tofts, C.: Describing social insect behaviour using process algebra. Transactions of the Society for Computer Simulation 9(4), 227-283 (1992)
22. Yoo, A.S., Greenwald, I.: LIN-12/Notch activation leads to microRNA-mediated down-regulation of Vav in C. elegans. Science 310, 1330-1333 (2005)