The genome of the medieval Black Death agent (extended abstract)

The genome of a 650 year old Yersinia pestis bacteria, responsible for the medieval Black Death, was recently sequenced and assembled into 2,105 contigs from the main chromosome. According to the point mutation record, the medieval bacteria could be an ancestor of most Yersinia pestis extant species, which opens the way to reconstructing the organization of these contigs using a comparative approach. We show that recent computational paleogenomics methods, aiming at reconstructing the organization of ancestral genomes from the comparison of extant genomes, can be used to correct, order and complete the contig set of the Black Death agent genome, providing a full chromosome sequence, at the nucleotide scale, of this ancient bacteria. This sequence suggests that a burst of mobile elements insertions predated the Black Death, leading to an exceptional genome plasticity and increase in rearrangement rate.Comment: Extended abstract of a talk presented at the conference JOBIM 2013, https://colloque.inra.fr/jobim2013_eng/. Full paper submitte

Comportements d'acteurs et dynamiques territoriales

National audienceNotre projet est de concevoir un outil d'aide à la décision en matière d'aménagement urbain, s'appliquant aux stratégies de localisation des entreprises commerciales. Il est basé sur la modélisation des interactions entre des acteurs (décideurs, groupes d'agents socio-économiques) et leur territoire. Deux idées fortes sous-tendent ce projet. La première est que l'espace représente un type d 'acteur particulier, qui agit sur le comportement des agents socio-économiques et qui, en retour, est modifié par eux. La seconde consiste à intégrer le raisonnement des équipes municipales (qui sont les décideurs en matière d'aménagement urbain) dans le modèle, afin d'obtenir un outil réellement utilisable par celles-ci

L'agglomération de Besançon a-t-elle une limite ?

La question des limites est récurrente en géographie : la limite permet de séparer un dedans, considéré comme homogène sous certains critères, d'un dehors, différent. Posé en ces termes, la question est simple. En fait, elle ne l'est pas du tout comme le montre la question de l'extension spatiale de l'agglomération bisontine. Quels sont les critères qui président à ce qui est ou non dans l'agglomération ? Des éléments de réponse convaincants sont apportés par la comparaison des résultats obtenus sur les périmètres du SCOT et de l'aire urbaine de Besançon

Sharing and disseminating knowledge of advanced spatial modeling. Presentation of an action carried out by the European research group s4 (spatial simulation for social sciences)

International audienceThe European research group S4 (Spatial simulation for social sciences) gathers researchers in geography as well as in geographical information sciences coming from about 30 European research centres. One action of the European research group S4 consists in sharing and disseminating knowledge of advanced spatial modelling. We propose here to describe several aspects of this action that are of interest considering the objectives of the CAENTI. The first aim of the action is to improve the diffusion of the results of the research in advanced spatial modelling, particularly in direction of regional and urban management and planning. The second aim is the development of tools and methods to improve coherence of knowledge and experiences that is especially required in those fields characterised by a rapidly developing research as it is the case for spatial systems analysis and modelling

iCrawl: Improving the Freshness of Web Collections by Integrating Social Web and Focused Web Crawling

Researchers in the Digital Humanities and journalists need to monitor, collect and analyze fresh online content regarding current events such as the Ebola outbreak or the Ukraine crisis on demand. However, existing focused crawling approaches only consider topical aspects while ignoring temporal aspects and therefore cannot achieve thematically coherent and fresh Web collections. Especially Social Media provide a rich source of fresh content, which is not used by state-of-the-art focused crawlers. In this paper we address the issues of enabling the collection of fresh and relevant Web and Social Web content for a topic of interest through seamless integration of Web and Social Media in a novel integrated focused crawler. The crawler collects Web and Social Media content in a single system and exploits the stream of fresh Social Media content for guiding the crawler.Comment: Published in the Proceedings of the 15th ACM/IEEE-CS Joint Conference on Digital Libraries 201

The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201