Gautier Stoll

Learn More
We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium"(More)
Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. There exist two major types of(More)
Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the formulation of new biological hypotheses to be tested, a fundamental principle of the systems biology approach. However, large-scale molecular maps are(More)
Ewing sarcoma is the second most frequent pediatric bone tumor. In most of the patients, a chromosomal translocation leads to the expression of the EWS-FLI1 chimeric transcription factor that is the major oncogene in this pathology. Relative genetic simplicity of Ewing sarcoma makes it particularly attractive for studying cancer in a systemic manner.(More)
We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g., the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic discrete dynamical models, we characterize the dynamical modifications in response to structural perturbations in the(More)
MOTIVATION The ability of cells to complete mitosis with high fidelity relies on elaborate checkpoint mechanisms. We study S- and M-phase checkpoint responses in silico in the budding yeast with a stochastic dynamical model for the cell-cycle. We aim to provide an unbiased functional classification of network interactions that reflect the contribution of(More)
We discuss the propagation of constraints in eukaryotic interaction networks in relation to model prediction and the identification of critical pathways. In order to cope with posttranslational interactions, we consider two types of nodes in the network, corresponding to proteins and to RNA. Microarray data provides very lacunar information for such types(More)
BACKGROUND A wide range of techniques is now available for analyzing regulatory networks. Nonetheless, most of these techniques fail to interpret large-scale transcriptional data at the post-translational level. RESULTS We address the question of using large-scale transcriptomic observation of a system perturbation to analyze a regulatory network which(More)
The segmentation of Drosophila is a prime model to study spatial patterning during embryogenesis. The spatial expression of segment polarity genes results from a complex network of interacting proteins whose expression products are maintained after successful segmentation. This prompted us to investigate the stability and robustness of this process using a(More)