A multi-scale constraint programming model of alternative splicing regulation

Theoretical Computer Science

Volumn 325, Issue 1, 2004, Pages 3-24

  Eveillard, Damien ^a,b   Ropers, Delphine ^b   De Jong, Hidde ^c   Branlant, Christiane ^b   Bockmayr, Alexander ^a  

^a LORIA   (France)

^b Biopôle de l Université de Lorraine   (France)

^c INRIA RHÔNE ALPES   (France)

Author keywords

Alternative splicing; Computational biology; Constraint programming; Hybrid system; Modeling

Indexed keywords

ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; CONSTRAINT PROGRAMMING; HYBRID SYSTEMS;

AMINO ACIDS; BIODIVERSITY; COMPUTER SIMULATION; CONSTRAINT THEORY; DNA; IMMUNOLOGY; MOLECULAR BIOLOGY; NUCLEIC ACIDS; PROTEINS; RNA;

COMPUTER PROGRAMMING;

EID: 4444276491     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2004.03.062     Document Type: Conference Paper

References (25)

1. Bernard O., Gouzé J.-L. Nonlinear qualitative signal processing for biological systems. application to the algal growth in bioreactors Math. Biosci. 157:1999;357-372.
2. A. Bockmayr, A. Courtois, Modeling biological systems in hybrid concurrent constraint programming (abstract), in: The Second Internat. Conf. Systems Biology, ICSB'01, Pasadena, CA, 2001, p. 106.
3. A. Bockmayr, A. Courtois, Using hybrid concurrent constraint programming to model dynamic biological systems, in: 18th Internat. Conf. on Logic Programming, ICLP'02, Copenhagen, Lecture Notes in Computer Science, Vol. 2401, Springer, Berlin, 2002, pp. 85-99.
4. Caputi M., Mayeda M., Krainer A., Zahler A. hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO. 18(14):1999;4060-4067.
5. B. Carlson, V. Gupta, Hybrid cc and interval constraints, in: Hybrid Systems: Computation and Control, HSCC'98, Lecture Notes in Computer Science, Vol. 1386, Springer, Berlin, 1998, pp. 80-95.
6. A. Audibert, D. Weil, F. Dautry, In vivo kinetics of mRNA splicing and transport in mammalian cells, Molecular Cell Biol. 22 (2002) 6706-6718.
7. Del Gatto-Konczak F., Olive M., Gesnel M., Breathnach R. hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Molecular Cell. Biol. 19(1):1999;251-260.
8. Graveley B. Sorting out the complexity of SR protein functions. RNA. 6:2000;1197-1211.
9. Gupta V., Jagadeesan R., Saraswat V. Computing with continuous change. Sci. Comput. Programming. 30(1-2):1998;3-49.
10. V. Gupta, R. Jagadeesan, V. Saraswat, D.G. Bobrow, Programming in hybrid constraint languages, in: Hybrid Systems II, Lecture Notes in Computer Science, Vol. 999, Springer, Berlin, 1995, pp. 226-251.
11. Hammond B. Quantitative study of the control of HIV-1 gene expression. J. Theoret. Biol. 163:1993;199-221.
12. Hartwell L., Hopfield J., Leibler S., Murray A. From molecular to modular cell biology. Nature. 402:1999;C47-C52.
13. Heinrich R., Schuster S. The Regulation of Cellular Systems. 1996;Thomson Publishing, New York.
14. Monod J. La technique des cultures continues. Théorie et applications. Ann. Inst. Pasteur. 79:1950;390-410.
15. M. Moore, C. Query, P. Sharp, Splicing of precursors to mRNA by the spliceosome, in: R. Gesteland, J. Atkins (Eds.), The RNA World, Cold Spring Harbor Laboratory Press, New York, 1993, pp. 303-357.
16. Murray J.D. Mathematical Biology I, An Introduction. 3rd Edition:2002;Springer, Berlin.
17. O'Reilly M., McNally M., Beemon K. Two strong 5' splice sites and competing, suboptimal 3' splice sites involved in alternative splicing of human immunodeficiency virus type 1 RNA. Virology. 213(2):1995;373-385.
18. Palsson B. The challenges of in silico biology. Natur. Biotechnol. 18:2000;1147-1150.
19. Purcell D., Martin M. Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity. J. Virol. 67(11):1993;6365-6378.
20. D. Ropers, Etude expérimentale du rôle des protéines SR dans la régulation de l'épissage de l'ARN du virus HIV-1, responsable de l'immunodéficience humaine, et modélisation mathématique de ces régulations, Ph.D. Thesis, University Henri Poincaré, Nancy, France.
21. D. Ropers, L. Ayadi, S. Jacquenet, A. Méreau, D. Thomas, A. Mougin, P. Bilodeau, M. Stolzfus, R. Gattoni, J. Stévenin, C. Branlant, Differential effects of the SR proteins 9G8, SC35, ASF/SF2 and SRp40 on the utilization of the A1 to A5 splicing sites of HIV-1 RNA, J. Biol. Chem., in press.
22. Saraswat V.A. Concurrent Constraint Programming. 1993;MIT Press, Cambridge, MA.
23. V.A. Saraswat, R. Jagadeesan, V. Gupta, Foundations of timed concurrent constraint programming, in: The Ninth Symp. Logic in Computer Science, LICS'94, Paris, IEEE, New York, 1994, pp. 71-80.
24. Saraswat V.A., Jagadeesan R., Gupta V. Timed default concurrent constraint programming. J. Symbol. Comput. 22(5/6):1996;475-520.
25. Tang H., Kuhen K., Wong-Staal F. Lentivirus replication and regulation. Annual Rev. Genet. 33:1999;133-170.