Modeling kohn interaction maps with beta-binders: An example

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

Volumn 3737 LNBI, Issue , 2005, Pages 33-48

  Ciocchetta, Federica ^a   Priami, Corrado ^a   Quaglia, Paola ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; PROTEINS; REDUCTION; SEMANTICS;

BETA BINDERS; DYNAMIC REPRESENTATION; KOHN MAPS;

CELLS;

EID: 37149036234     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11599128_3     Document Type: Conference Paper

References (16)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. Molecular biology of the cell (IV ed.). Garland science, 2002.
2. L. Cardelli. Membrane interactions. In BioConcur '03, Workshop on Concurrent Models in Molecular Biology, 2003.
3. V. Danos and J. Krivine. Formal molecular biology done in CCS-R. In BioConcur '03, Workshop on Concurrent Models in Molecular Biology, 2003.
4. V. Danos and C. Laneve. Core formal molecular biology. In P. Degano, editor, Proc. 12th European Symposium on Programming (ESOP '03), volume 2618 of Lecture Notes in Computer Science. Springer, 2003.
5. M.L. Guerriero. Modelli formali per la rappresentazione di sistemi biologici dinamici. Laurea Thesis, University of Trento, Dep. Informatics and Telecommunications (In Italian), 2004.
6. K.W. Kohn. Molecular interaction map of the mammalian cell cycle contro and DNA repair systems. Molecular Biology of the Cell, (10):2703-2734, 1999.
7. D. Lane. Surfing the p53 network. Nature, 408:307-10, 2000.
8. D. Lane, B. Vogelstein, and A.J. Levine. P53, the guardian of the genome. Nature, 358:15-16, 1992.
9. R. Milner. Communicating and mobile systems: the π-calculus. Cambridge Universtity Press, 1999.
10. M. Nagasaki, S. Onami, S. Miyano, and H. Kitano. Bio-calculus: Its concept and molecular interaction. In K. Asai, S. Miyano, and T. Takagi, editors, Genome Informatics 1999, volume 10, pages 133-143. Universal Academy Press, 1999.
11. C. Priami and P. Quaglia. Beta binders for biological interactions. In Proc. CMSB '04, Lecture Notes in Bioinformatics. Springer, 2004. To appear.
12. C. Priami and P. Quaglia. Operational patterns in Beta-binders. Transactions on Computational Systems Biology, 2004. To appear.
13. C. Priami, A. Regev, W. Silverman, and E. Shapiro. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80(1):25-31, 2001.
14. A. Regev, E.M. Panina, W. Silverman, L. Cardelli, and E. Shapiro. Bioambients: An abstraction for biological compartments. Theoretical Computer Science, 2004. To appear.
15. A. Regev, W. Silverman, and E. Shapiro. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Proc. of the Pacific Symposium on Biocomputing (PSB '01), volume 6, pages 459-470. World Scientific Press, 2001.
16. D. Sangiorgi and D. D. Walker. The π-calculus: a Theory of Mobile Processes. Cambridge Universtity Press, 2001.