Graph transformation in molecular biology

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

Volumn 3393 LNCS, Issue , 2005, Pages 116-133

  Rosselló, Francesc ^a   Valiente, Gabriel ^b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ENGINEERING; COMPUTATIONAL GRAMMARS; MATHEMATICAL TRANSFORMATIONS; MOLECULAR BIOLOGY;

BIOLOGICAL APPLICATIONS; GRAPH TRANSFORMATION; HIGHER-DIMENSIONAL STRUCTURES;

GRAPH THEORY;

EID: 34548512573     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-31847-7_7     Document Type: Article

References (71)

1. Abe, N., Mamitsuka, H.: Predicting protein secondary structure using stochastic tree grammars. Machine learning 29 (1997) 275-301
2. Beck, M., Benkö, G., G. Eble, C.F., Müller, S., Stadler, P.: Graph grammars as models for the evolution of developmental pathways. In Schaub, H., Detje, F., Brüggemann, U., eds.: The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, IOS Press (2004) 8-15
3. Benkö, G., Flamm, C., Stadler, P.F.: A graph-based toy model of chemistry. Journal of Chemical Information and Computer Sciences 43 (2003) 1085-1093
4. Benkö, G., Flamm, C., Stadler, P.F.: Multi-phase artificial chemistry. In Schaub, H., Detje, F., Brüggemann, U., eds.: The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, IOS Press (2004) 16-22
5. Benkö, G., Flamm, C., Stadler, P.F.: Generic properties of chemical networks: Artificial chemistry based on graph rewriting. In: Proc. 7th European Conf. Advances in Artificial Life. Volume 2801 of Lecture Notes in Computer Science., Springer-Verlag (2003) 10-19
6. Bower, J.M., H. Bolouri, e.: Computational modeling of genetic and biochemical networks. MIT Press, Cambridge, MA (2001)
7. Brendel, V., Busse, H.G.: Genome structure described by formal languages. Nucleic Acid Research 12 (1984) 2561-2568
8. Cardelli, L.: Brane calculi. In: Proc. Workshop Concurrent Methods in Molecular Biology. Electronic Notes in Theoretical Computer Science, Elsevier (2004) to appear.
9. Cayley, A.: On the mathematical theory of isomers. Philosophical Magazine 47 (1874) 444-446
10. Chan, H.S., Dill, K.A.: Compact polymers. Macromolecules 22 (1989) 4559-4573
11. Corradini, A., Montanari, U., Rossi, F., Ehrig, H., Heckel, R., Löwe, M.: Algebraic approaches to graph transformation. Part I: Basic concepts and double pushout approach. In Rozenberg, G., ed.: Handbook of Graph Grammars and Computing by Graph Transformation, Volume 1: Foundations. World Scientific (1997) 163-246
12. Culik II, K., Lindenmayer, A.: Parallel rewriting on graphs and multidimensional development. Int. Journ. of General Systems 3 (1976) 53-66
13. Curti, M., Degano, P., Baldari, C.: Causal π-calculus for biochemical modelling. In: Proc. 1st Int. Workshop Computational Methods in Systems Biology. Volume 2602 of Lecture Notes in Computer Science., Springer-Verlag (2003) 21-33
14. Danos, V., Krivine, J.: Formal molecular biology done in CCS. In: Proc. Workshop Concurrent Methods in Molecular Biology. Electronic Notes in Theoretical Computer Science, Elsevier (2004) to appear.
15. Danos, V., Laneve, C.: Graphs for core molecular biology. In: Proc. 1st Int. Workshop Computational Methods in Systems Biology. Volume 2602 of Lecture Notes in Computer Science., Springer-Verlag (2003) 34-46
16. Danos, V., Laneve, C.: Core formal molecular biology. In: Proc. 12th European Symposium on Programming. Volume 2618 of Lecture Notes in Computer Science., Springer-Verlag (2003) 302-318
17. Danos, V., Laneve, C.: Formal molecular biology. Theoretical Computer Science 325 (2004) 69-110
18. Deville, Y., Gilbert, D., van Helden, J., Wodak, S.J.: An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4 (2003) 246-259
19. Fringuelli, F., Taticchi, A.: The Diels-Alder Reaction: Selected Practical Methods. John Wiley & Sons, Chichester, England (2002)
20. Dittrich, P., Ziegler, J., Banzhaff, W.: Artificial chemistries - a review. Artificial life 7 (2001) 225-275
21. Durbin, R., Krogh., A., Mitchison, G., Eddy, S.: Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge Univ. Press, Cambridge (1998)
22. Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rosenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Natural computing series. Springer-Verlag, Berlin (2004)
23. Ehrig, H., Heckel, R., Korff, M., Löwe, M., Ribeiro, L., Wagner, A., Corradini, A.: Algebraic approaches to graph transformation, part II: Single pushout approach and comparison with double pushout approach. In Rozenberg, G., ed.: Handbook of Graph Grammars and Computing by Graph Transformation. Volume 1: Foundations. World Scientific (1997) 247-312
24. Ehrig, H., Mahr, B.: Fundamentals of algebraic specification I: Equations and initial semantics. Springer Verlag (1985)
25. Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sonmez, K.: Pathway logic: Symbolic analisys of biological signalling. In: Pacific symposium on Biocomputing 2001, World Scientific (2001) 400-412
26. Fan, L.T., Bertók, B., Friedler, F.: A graph-theoretic method to identify candidate mechanisms for deriving the rate law of a catalytic reaction. Computers & Chemistry 26 (2002) 265-292
27. Félix, L., Rosselló, F., Valiente, G.: Artificial chemistries and metabolic pathways. In Messeguer, X., Valiente, G., eds.: Proc. 5th Annual Spanish Bioinformatics Conference, Barcelona, Technical University of Catalonia (2004) 56-59
28. Flamm, C., Fontana, W., Hofacker, I., Schuster, P.: Kinetic folding of RNA at elementary step resolution. RNA 6 (2000) 325-338
29. Fontana, W.: Algorithmic chemistry. In: Artificial Life II. Volume 47 of Santa Fe Institute Studies in the Sciences of Complexity., Addison-Wesley (1992) 159-210
30. Fujita, S.: Description of organic reactions based on imaginary transition structures. Part 1-5. Journal of Chemical Information and Computer Sciences 26 (1986) 205-242
31. Fujita, S.: Computer-Oriented Representation of Organic Reactions. Yoshioka Shoten, Kyoto (2001)
32. Fujita, S.: Description of organic reactions based on imaginary transition structures. Part 6-9. Journal of Chemical Information and Computer Sciences 27 (1987) 99-120
33. Gernert, D.: Graph grammars as an analytical tool in physics and biology. Biosystems 43 (1997) 179-187
34. Goss, P., Peccoud, J.: Quantitative modelling of stochastic systems in molecular biology using stochastic Petri nets. Proc. Nat. Acad. Sc. 95 (1998) 6750-6755
35. Heckel, R., Lajios, G., Menge, S.: Stochastic graph transformation systems. In: Proc. 2nd Int. Conf. Graph Transformation. Volume 3256 of Lecture Notes in Computer Science., Springer-Verlag (2004) 210-225
36. Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, L., Tacker, M., Schuster, P.: Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125 (1994) 167-188
37. Kanehisa, M., Goto, S.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28 (2000) 27-30
38. Kister, A., Magarshak, Y., Malinsky, J.: The theoretical analysis of the process of RNA molecule self-assembly. BioSystems 30 (1993) 31-48
39. Kitano, H.: Computational systems biology. Nature 420 (2002) 206-210
40. Lesk, A.M.: Systematic representation of protein folding patterns. J. Mol. Graph. 13 (1995) 159-164
41. Mayoh, B.: On patterns and graphs. Preprint (1995)
42. Mayoh, B.: Multidimensional Lindenmayer organisms. In: L-systems. Volume 15 of Lecture Notes in Computer Science., Springer-Verlag (1974) 302-326
43. McAdams, H., Arkin, A.: It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics 15 (1999) 65-69
44. McCaskill, J., Niemann, U.: Graph replacement chemistry for DNA processing. In: Proc. 6th Int. Workshop DNA-Based Computers. Volume 2054 of Lecture Notes in Computer Science., Springer-Verlag (2001) 103-116
45. Michal, G., ed.: Biological Pathways: An Atlas of Biochemistry and Molecular Biology. John Wiley & Sons, New York (1999)
46. Polanski, O.: Graphs in quantum chemistry. MATCH 1 (1975) 183-195
47. Priami, C., ed.: Proc. 1st Int. Workshop Computational Methods in Systems Biology. Volume 2602 of Lecture Notes in Computer Science., Springer-Verlag (2003)
48. Przytycka, T., Srinivasan, T., Rose, G.: Recursive domains in proteins. Protein Science 11 (2002) 409-417
49. Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π- calculus process algebra. In: Pacific symposium on Biocomputing 2001, World Scientific (2001) 459-470
50. Regev, A., Shapiro, E.: Cells as computation. Nature 419 (2002) 343
51. Reidys, C., Stadler, P.F.: Bio-molecular shapes and algebraic structures. Computers & Chemistry 20 (1996) 85-94
52. Richardson, J.: β-sheet topology and the relatedness of proteins. Nature 268 (1977) 495-500
53. Rivas, E., Eddy, S.R.: The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 16 (2000) 334-340
54. Rosselló, F., Valiente, G.: Chemical graphs, chemical reaction graphs, and chemical graph transformation. In: Proc. 2nd Int. Workshop Graph-Based Tools. Electronic Notes in Theoretical Computer Science, Elsevier (2004) to appear.
55. Rosselló, F., Valiente, G.: Analysis of metabolic pathways by graph transformation. In: Proc. 2nd Int. Conf. Graph Transformation. Volume 3256 of Lecture Notes in Computer Science., Springer-Verlag (2004) 70-82
56. Sakakibara, Y., Brown, M., Hughey, R., Mian, I., Sjolander, K., Underwood, R., Haussler, D.: Stochastic context-free grammars for tRNA modeling. Nucleic Acids Research 22 (1994) 5112-5128
57. Schultz, J., Milpetz, F., Bork, P., Ponting, C.: SMART, a simple molecular architecture research tool. Proc. Nat. Acad. Sc. 95 (1998) 5857-5864
58. Searls, D.: The computational linguistics of biological sequences. In: Artificial Intelligence and Molecular Biology, AAAI Press (1993) 47-120
59. Searls, D.: Formal language and biological macromolecules. In: Mathematical Support for Molecular Biology. Volume 47 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science., AMS (1999) 128-141
60. Searls, D.: The language of genes. Nature 420 (2002) 211-217
61. Seo, H., Lee, D.Y., Park, S., Fan, L.T., Shafie, S., Bertók, B., Friedler, F.: Graph-theoretical identification of pathways for biochemical reactions. Biotechnology Letters 23 (2001) 1551-1557
62. Speroni, P.: Artificial chemistries. Bull. EATCS 76 (2002) 128-141
63. Tomita, K., Kurokawa, H., Murata, S.: Graph automata: natural expression of self reproduction. Physica D 171 (2002) 197-210
64. Waterman, M.S., Smith, T.F.: RNA secondary structure: a complete mathematical analysis. Math. Biosci. 42 (1978) 257-266
65. Weininger, D.: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences 28 (1988) 31-36
66. Weininger, D., Weininger, A., Weininger, J.L.: SMILES. 2. Algorithm for generation of unique SMILES notation. Journal of Chemical Information and Computer Sciences 29 (1989) 97-101
67. Weininger, D.: SMILES. 3. DEPICT. Graphical depiction of chemical structures. Journal of Chemical Information and Computer Sciences 30 (1990) 237-243
68. Westhead, D., Slidel, T., Flores, T., Thornton, J.: Protein structural topology: automated analysis and diagrammatic representation. Protein Science 8 (1999) 897-904
69. Yadav, M.K., Kelley, B.P., Silverman, S.M.: The potential of a chemical graph transformation system. In: Proc. 2nd Int. Conf. Graph Transformation. Volume 3256 of Lecture Notes in Computer Science., Springer-Verlag (2004) 83-95
70. Zevedei-Oancea, I., Schuster, S.: Topological analysis of metabolic networks based on Petri net theory. In Silico Biology 3 (2003) 323-345
71. Zuker, M., Sankoff, D.: RNA secondary structures and their prediction. Bull. Math. Biol. 46 (1984) 591-621