Sainte-Foy-lès-Lyon, France
Sainte-Foy-lès-Lyon, France

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Grauwin S.,University of Lyon | Grauwin S.,Rhone Alpes Institute of Complex Systems | Grauwin S.,CNRS Physics Laboratory | Beslon G.,University of Lyon | And 14 more authors.
Journal of the American Society for Information Science and Technology | Year: 2012

Using a large database (∼215,000 records) of relevant articles, we empirically study the complex systems field and its claims to find universal principles applying to systems in general. The study of references shared by the articles allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory, but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones," i.e., subcommunities that create an interface around specific tools (a DNA microchip) or concepts (a network). © 2012 ASIS&T.

Boulos R.E.,University of Lyon | Boulos R.E.,French National Center for Scientific Research | Julienne H.,University of Lyon | Julienne H.,French National Center for Scientific Research | And 16 more authors.
New Journal of Physics | Year: 2014

The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are 'master' replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of selfinteracting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/ U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that 'master' replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Boulos R.E.,University of Lyon | Boulos R.E.,French National Center for Scientific Research | Arneodo A.,University of Lyon | Arneodo A.,French National Center for Scientific Research | And 5 more authors.
Physical Review Letters | Year: 2013

We use graph theory to analyze chromatin interaction (Hi-C) data in the human genome. We show that a key functional feature of the genome - "master" replication origins - corresponds to DNA loci of maximal network centrality. These loci form a set of interconnected hubs both within chromosomes and between different chromosomes. Our results open the way to a fruitful use of graph theory concepts to decipher DNA structural organization in relation to genome functions such as replication and transcription. This quantitative information should prove useful to discriminate between possible polymer models of nuclear organization. © 2013 American Physical Society.

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