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Cointet J.-P.,University Paris Est Creteil | Cointet J.-P.,Institute des Systemes Complexes | Mogoutov A.,University Paris Est Creteil | Bourret P.,Aix - Marseille University | And 2 more authors.
Medecine/Sciences | Year: 2012

This paper examines the emergence and development of one of the key components of genomics, namely gene expression profiling. It does so by resorting to computer-based methods to analyze and visualize networks of scientific publications. Our results show the central role played by oncology in this domain, insofar as the initial proofof-principle articles based on a plant model organism have quickly led to the demonstration of the value of these techniques in blood cancers and to applications in the field of solid tumors, and in particular breast cancer. The article also outlines the essential role played by novel bioinformatics and biostatistical tools in the development of the domain. These computational disciplines thus qualify as one of the three corners (in addition to the laboratory and the clinic) of the translational research triangle. Source

Auger P.,Center Ird Of Lile Of France | Lett C.,Institute des Systemes Complexes | Moussaoui A.,Abou Bekr Belkaid University Tlemcen | Pioch S.,Caisse des Depots Co
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2010

We present a mathematical model of artificial pelagic multisite fisheries. The model is a stock-effort dynamical model of a fishery subdivided into artificial fishing sites such as fish-aggregating devices (FADs) or artificial habitats (AHs). The objective of the work is to investigate the effects of the number of sites on the global activity of the fishery. We consider a linear chain of fishing sites in which fish are harvested by fishing vessels and a free stock that is unattached to the sites and not exploited. Fish movements between the sites and the free stock, as well as vessel displacements between the sites, are assumed to take place at a faster time scale than the variation of the stock and the change of the fleet size. We take advantage of these two time scales to derive a reduced model governing the dynamics of the total fish stock and the total fishing effort. We show that there exists an optimal number of fishing sites that maximizes the total catch at equilibrium. We finally extend the model to the situation in which both fish attached to the sites and fish in the free stock are exploited. Source

Possoz C.,French National Center for Scientific Research | Junier I.,Institut Universitaire de France | Junier I.,Institute des Systemes Complexes | Espeli O.,French National Center for Scientific Research
Frontiers in Bioscience | Year: 2012

Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with model organisms: Escherichia coli, Bacillus subtilis, Caulobacter crescentus and Vibrio cholerae. We describe the global positionning of the nucleoid in the cell and the specific localization and dynamics of different chromosomal loci, kinetic and biophysic aspects of chromosome segregation are presented. Finally, a presentation of the key proteins involved in the chromosome segregation is made. Source

Reuillon R.,Institute des Systemes Complexes | Leclaire M.,Institute des Systemes Complexes | Passerat-Palmbach J.,Imperial College London
Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015 | Year: 2015

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. In this work, we briefly expose the strong assets of OpenMOLE and demonstrate its efficiency at exploring the parameter set of an agent simulation model. We perform a multi-objective optimisation on this model using computationally expensive Genetic Algorithms (GA). OpenMOLE hides the complexity of designing such an experiment thanks to its DSL, and transparently distributes the optimisation process. The example shows how an initialisation of the GA with a population of 200,000 individuals can be evaluated in one hour on the European Grid Infrastructure. © 2015 IEEE. Source

Castro-Gonzalez C.,Technical University of Madrid | Castro-Gonzalez C.,CIBER ISCIII | Castro-Gonzalez C.,Massachusetts Institute of Technology | Luengo-Oroz M.A.,Technical University of Madrid | And 21 more authors.
PLoS Computational Biology | Year: 2014

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages. © 2014 Castro-González et al. Source

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