Search Results - "Kepes, Francois"

A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data by Le Treut, Guillaume, Képès, François, Orland, Henri

“…It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example, coregulated genes in several…”
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Thermodynamics of Long Supercoiled Molecules: Insights from Highly Efficient Monte Carlo Simulations by Lepage, Thibaut, Képès, François, Junier, Ivan

“…Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis…”
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Spatial and topological organization of DNA chains induced by gene co-localization by Junier, Ivan, Martin, Olivier, Képès, François

“…Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular,…”
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Phase Behavior of DNA in the Presence of DNA-Binding Proteins by Le Treut, Guillaume, Képès, François, Orland, Henri

“…To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of nonspecific binding proteins, we implemented a Flory-Huggins free…”
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Analysis tools for the interplay between genome layout and regulation by Bouyioukos, Costas, Elati, Mohamed, Képès, François

“…Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome…”
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CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus by Junier, Ivan, Dale, Ryan K, Hou, Chunhui, Képès, François, Dean, Ann

“…The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to…”
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Topological and causal structure of the yeast transcriptional regulatory network by Bottani, Samuele, Bourgine, Paul, Képès, François, Guelzim, Nabil

“…Interpretation of high-throughput biological data requires a knowledge of the design principles underlying the networks that sustain cellular functions. Of…”
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GREAT: a web portal for Genome Regulatory Architecture Tools by Bouyioukos, Costas, Bucchini, François, Elati, Mohamed, Képès, François

“…GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome…”
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From multiple pathogenicity islands to a unique organized pathogenicity archipelago by Bouyioukos, Costas, Reverchon, Sylvie, Képès, François

“…Pathogenicity islands are sets of successive genes in a genome that determine the virulence of a bacterium. In a growing number of studies, bacterial virulence…”
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Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies by Junier, Ivan, Hérisson, Joan, Képès, François

“…The need for efficient molecular interplay in time and space within a cell imposes strong constraints that could be partially relaxed if relative gene…”
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The layout of a bacterial genome by Képès, François, Jester, Brian C., Lepage, Thibaut, Rafiei, Nafiseh, Rosu, Bianca, Junier, Ivan

“…Recently the mismatch between our newly acquired capacity to synthetize DNA at genome scale, and our low capacity to design ab initio a functional genome has…”
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PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION by Elati, Mohamed, Nicolle, Rémy, Junier, Ivan, Fernández, David, Fekih, Rim, Font, Julio, Képès, François

“…Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a…”
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Periodic pattern detection in sparse boolean sequences by Junier, Ivan, Hérisson, Joan, Képès, François

“…The specific position of functionally related genes along the DNA has been shown to reflect the interplay between chromosome structure and genetic regulation…”
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Synthetic and integrative biology by Képès, François

“…Integrative biology currently undergoes a deep renewal as we witness the increasing influence of systems biology, which explores life's logic, and of synthetic…”
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Compositional complementarity and prebiotic ecology in the origin of life by Hunding, Axel, Kepes, Francois, Lancet, Doron, Minsky, Abraham, Norris, Vic, Raine, Derek, Sriram, K., Root-Bernstein, Robert

“…We hypothesize that life began not with the first self‐reproducing molecule or metabolic network, but as a prebiotic ecology of co‐evolving populations of…”
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Scientific and technological conditions of the emergence of synthetic biology by Képès, François

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Incremental and unifying modelling formalism for biological interaction networks by Yartseva, Anastasia, Klaudel, Hanna, Devillers, Raymond, Képès, François

“…An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological…”
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The adaptive filter of the yeast galactose pathway by Smidtas, Serge, Schächter, Vincent, Képès, François

“…In the yeast Saccharomyces cerevisiae, the interplay between galactose, Gal3p, Gal80p and Gal4p determines the transcriptional status of the genes required for…”
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Model of interactions in biology and application to heterogeneous network in yeast by Smidtas, Serge, Yartseva, Anastasia, Schächter, Vincent, Képès, François

“…A major challenge for bioinformatics and theoretical biology is to build and analyse a unified model of biological knowledge resulting from high-throughput…”
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First French team success during iGEM synthetic biology competition by Bikard, David, Képès, François

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