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Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract)

Damien Eveillard 1 Arnaud Courtois 1 Alexander Bockmayr 1
1 MODBIO - Computational models in molecular biology
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : Alternative splicing is a biological process occurring in post-transcriptional regulation of RNA. Through the elimination of selected introns, alternative splicing allows the generation of several kinds of mature RNA from the same premessenger RNA. The resulting combinatorial complexity contributes to biological diversity, especially in the case of the human immunodeficiency virus (HIV-1). Recent biological studies show the impact that SR proteins have on the dynamics of post-transcriptional regulation via the control of the splicing process. Constraint programming seems well-suited for modeling alternative splicing regulation because it allows one to handle partial or incomplete information. Each constraint gives one piece of information on the system that is studied. The overall knowledge is accumulated in the constraint store. Using a hybrid constraint programming (hybrid cc) approach, we develop a model of the alternative splicing regulation in HIV-1. Our model integrates different scales (single splicing site vs.\ multiple splicing sites), and thus allows us to exploit several types of experimental data available to us. The ultimate goal is to obtain a model that can be validated qualitatively both on the scale of a single splicing site and on the scale of the whole HIV-1, in order to represent the global effect of alternative splicing in the HIV-1 cycle.
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https://hal.inria.fr/inria-00099705
Contributor : Publications Loria <>
Submitted on : Tuesday, September 26, 2006 - 9:40:29 AM
Last modification on : Monday, February 17, 2020 - 3:50:19 PM

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  • HAL Id : inria-00099705, version 1

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Damien Eveillard, Arnaud Courtois, Alexander Bockmayr. Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract). Modeling and Simulation of Biological Regulatory Processes - ECCB Satellite Meeting, 2003, Paris, France. ⟨inria-00099705⟩

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