Multiscale Modeling of Alternative Splicing Regulation

Alternative splicing is a key process in post-transcriptional regulation, by which several kinds of mature RNA can be obtained from the same premessenger RNA. Using a constraint programming approach, we model the alternative splicing regulation at different scales (single site vs. multiple sites), thus exploiting different types of available experimental data.

[1]  B. Hammond,et al.  Quantitative study of the control of HIV-1 gene expression. , 1993, Journal of theoretical biology.

[2]  A. Staffa,et al.  The tat/rev intron of human immunodeficiency virus type 1 is inefficiently spliced because of suboptimal signals in the 3' splice site , 1994, Journal of virology.

[3]  Radha Jagadeesan,et al.  Computing with Continuous Change , 1998, Sci. Comput. Program..

[4]  M. Olive,et al.  hnRNP A1 Recruited to an Exon In Vivo Can Function as an Exon Splicing Silencer , 1999, Molecular and Cellular Biology.

[5]  Jean-Luc Gouzé,et al.  TRANSIENT BEHAVIOR OF BIOLOGICAL MODELS AS A TOOL OF QUALITATIVE VALIDATION—APPLICATION TO THE DROOP MODEL AND TO A N-P-Z MODEL , 1996 .

[6]  K. Kuhen,et al.  Lentivirus replication and regulation. , 1999, Annual review of genetics.

[7]  R. Heinrich,et al.  The Regulation of Cellular Systems , 1996, Springer US.

[8]  Alexander Bockmayr,et al.  Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems , 2002, ICLP.

[9]  Phillip A. Sharp,et al.  13 Splicing of Precursors to mRNA by the Spliceosome , 1993 .

[10]  A. Zahler,et al.  hnRNP A/B proteins are required for inhibition of HIV‐1 pre‐mRNA splicing , 1999, The EMBO journal.

[11]  Modelling dynamic phenomena in molecular and cellular biology , 1986 .

[12]  B. Palsson.  The challenges of in silico biology , 2000, Nature Biotechnology.

[13]  Alexander Bockmayr,et al.  Modeling biological systems in hybrid concurrent constraint programming (Poster abstract) , 2001 .

[14]  Vijay A. Saraswat,et al.  Concurrent constraint programming , 1989, POPL '90.

[15]  Radha Jagadeesan,et al.  Timed Default Concurrent Constraint Programming , 1996, J. Symb. Comput..

[16]  T. Maniatis,et al.  A systematic analysis of the factors that determine the strength of pre‐mRNA splicing enhancers , 1998, The EMBO journal.

[17]  Lee A. Segel,et al.  Modeling Dynamic Phenomena in Molecular and Cellular Biology , 1984 .

[18]  Radha Jagadeesan,et al.  Foundations of timed concurrent constraint programming , 1994, Proceedings Ninth Annual IEEE Symposium on Logic in Computer Science.

[19]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[20]  B. Amendt,et al.  Splicing efficiency of human immunodeficiency virus type 1 tat RNA is determined by both a suboptimal 3' splice site and a 10 nucleotide exon splicing silencer element located within tat exon 2. , 1997, Nucleic acids research.

[21]  K. Beemon,et al.  Two strong 5' splice sites and competing, suboptimal 3' splice sites involved in alternative splicing of human immunodeficiency virus type 1 RNA. , 1995, Virology.

[22]  C. Stoltzfus,et al.  The Exon Splicing Silencer in Human Immunodeficiency Virus Type 1 Tat Exon 3 Is Bipartite and Acts Early in Spliceosome Assembly , 1998, Molecular and Cellular Biology.

[23]  Daniel G. Bobrow,et al.  Programming in Hybrid Constraint Languages , 1994, Hybrid Systems.

[24]  Robert L. Grossman,et al.  Timed Automata , 1999, CAV.

[25]  D. Purcell,et al.  Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity , 1993, Journal of virology.

[26]  B. Graveley.  Sorting out the complexity of SR protein functions. , 2000, RNA.

[27]  James W. Haefner,et al.  Modeling Biological Systems , 1996, Springer US.