- Periodic transcriptional organization of the E.coli genomeFrancois Kepes
ATelier de Génomique Cognitive, CNRS UMR8071 genopole, Evry, France
J Mol Biol 340:957-64. 2004..Binding at genuine regulatory sites on DNA would thus be optimized by co-transcriptionally translating regulators in their vicinity...
- Modelling macromolecular networks: two meetings in Paris, July, 2002Francois Kepes
ATelier de Génomique Cognitive, CNRS ESA8071 genopole, Evry, France
Bioessays 24:1188-90. 2002
- Membrane traffic in virtual realityFrancois Kepes
Dynamique de la Compartimentation Cellulaire, Institut des Sciences du Vegetal, CNRS UPR2355, Gif sur Yvette and ATelier de Génomique Cognitive, CNRS ESA8071 genopole R, Evry, France
Traffic 4:13-7. 2003
- Secretory compartments as instances of dynamic self-evolving structuresFrancois Kepes
ATelier de Génomique Cognitive, CNRS ESA8071 genopole, 523 Terrasses de l Agora, 91000 Evry, France
Acta Biotheor 50:209-21. 2002..This model is extended to briefly outline three evolutionary "inventions", from S. cerevisiae to another yeast, Pichia pastoris, on to plant, and on to animal cells: stacking, stabilizing and aggregating the primary Golgi elements...
- Periodic epi-organization of the yeast genome revealed by the distribution of promoter sitesFrancois Kepes
ATelier de Génomique Cognitive, CNRS UMR8071 genopole, 523 Terrasses de l Agora, 91000 Evry, France
J Mol Biol 329:859-65. 2003..In this model, self-organization of transcriptional initiation plays a major role in the functional nuclear architecture...
- [Epigenetics as an aspect of post-genomics]Francois Kepes
Programme d Epigénomique, Genopole, ATelier de Génomique Cognitive, CNRS UMR 8071 Genopole, 93, rue Henri Rochefort, 91000 Evry, France
Med Sci (Paris) 21:371-6. 2005..g. a differentiated state that results from tipping a regulatory "toggle switch", involve components that are distributed throughout the nucleus or the cytoplasm, and possibly all the way to cell confines...
- Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replicationNicolas Omont
ATGC, CNRS UMR 8071 Genopole, 523 Terrasses de l Agora, 91000 Evry, France
Bioinformatics 20:2719-25. 2004..This model is validated by an analysis of proven and predicted units in Escherichia coli and Bacillus subtilis. The results are consistent with an equal cost of head-on versus codirectional collisions...
- Effects of brefeldin A and nordihydroguaiaretic acid on endomembrane dynamics and lipid synthesis in plant cellsPatricia Merigout
Laboratoire de Dynamique de la Compartimentation Cellulaire, Institut des Sciences du Vegetal, CNRS UPR 2355, 91198 Cedex, Gif sur Yvette, France
FEBS Lett 518:88-92. 2002..The importance of phytosterols in membrane architecture and membrane trafficking is discussed...
- Topological and causal structure of the yeast transcriptional regulatory networkNabil Guelzim
ATelier de Génomique Cognitive, Centre National de la Recherche Scientifique ESA 8071, Genopole R, 523 Terrasses de l Agora, 91000 Evry, France
Nat Genet 31:60-3. 2002..This deviation from randomness probably reflects functional constraints that include biosynthetic cost, response delay and differentiative and homeostatic regulation...
- PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positIONMohamed Elati
Institute of Systems and Synthetic Biology, CNRS, University of Evry, Genopole, 91030 Evry, France
Nucleic Acids Res 41:1406-15. 2013..The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases...
- Genomic organization of evolutionarily correlated genes in bacteria: limits and strategiesIvan Junier
Epigenomics Project Institute of Systems and Synthetic Biology, Genopole, CNRS, University of Evry, 91030 Evry, France
J Mol Biol 419:369-86. 2012..The transition at 20 genes is reminiscent of the size of the longest operons and of topological microdomains. The range for which DNA neighborhood optimizes biochemical interactions might therefore be defined by DNA topology...
- Morphodynamics of the secretory pathwayFrancois Kepes
ATelier de Génomique Cognitive, CNRS UMR 8071 Genopole and Epigenomics Project, Genopole, Evry, France
Int Rev Cytol 242:55-120. 2005..Nonequilibrium secretory structures would provide yeasts, and plants to a lesser extent, with the required versatility to cope with ever changing environments, by contrast to the stabler milieu intérieur of homeothermic animals...
- Spatial and topological organization of DNA chains induced by gene co-localizationIvan Junier
Epigenomics Project, Genopole, CNRS UPS 3201, UniverSud Paris, University of Evry, Genopole Campus 1 Genavenir 6, Evry, France
PLoS Comput Biol 6:e1000678. 2010....
- GREAT: a web portal for Genome Regulatory Architecture ToolsCostas Bouyioukos
iSSB, CNRS, Genopole, UEVE, Université Paris Saclay, 5 rue Henri Desbrueres, Evry 91030 Cedex, France
Nucleic Acids Res 44:W77-82. 2016..The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. ..
- Analysis tools for the interplay between genome layout and regulationCostas Bouyioukos
Institute of Systems and Synthetic Biology ISSB, Genopole, CNRS, Universite d Evry Val d Essonne, Evry, France
BMC Bioinformatics 17:191. 2016..Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes...
- Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulationsThibaut Lepage
Institute of Systems and Synthetic Biology, Genopole, CNRS, University of Evry, Evry, France Laboratoire Adaptation et Pathogénie des Micro organismes UMR 5163, Université Grenoble 1, CNRS, Grenoble, France
Biophys J 109:135-43. 2015..As an example, we report values that are in good agreement with experiments and that concern the longest molecules that have been studied so far (16 kbp). ..
- CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locusIvan Junier
Epigenomics Project and institute of Systems and Synthetic Biology, Genopole, CNRS, University of Evry, 5 rue Henri Desbrueres, Evry F 91030, Institute of Complex Systems, Paris, France
Nucleic Acids Res 40:7718-27. 2012..Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription...
- Periodic pattern detection in sparse boolean sequencesIvan Junier
Epigenomics Project, Genopole, CNRS UPS3201, UniverSud Paris, University of Evry, Genopole Campus 1 Genavenir 6, 5 rue Henri Desbruères F 91030 EVRY cedex, France
Algorithms Mol Biol 5:31. 2010..e. sequences of the type 010011011010... where the ratio of the number of 1's (denoting here the transcription start of a gene) to 0's is small...
- [Synthetic and integrative biology]Francois Kepes
Genopole, CNRS, Université d Evry, Evry, France
Med Sci (Paris) 25:39-42. 2009..Integrative biology currently undergoes a deep renewal as we witness the increasing influence of systems biology, which explores life's logic, and of synthetic biology, which exploits it...
- The adaptive filter of the yeast galactose pathwaySerge Smidtas
Genoscope Centre National de Séquençage, CNRS UMR8030, 2 rue Gaston Cremieux, 91000 Evry, France
J Theor Biol 242:372-81. 2006..Finally, this feedback loop, by allowing phosphorylation of some active Gal4p, may be essential to initiate the subsequent long-term response...