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<OAI-PMH schemaLocation=http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd> <responseDate>2018-01-15T18:21:32Z</responseDate> <request identifier=oai:HAL:hal-01379033v1 verb=GetRecord metadataPrefix=oai_dc>http://api.archives-ouvertes.fr/oai/hal/</request> <GetRecord> <record> <header> <identifier>oai:HAL:hal-01379033v1</identifier> <datestamp>2018-01-11</datestamp> <setSpec>type:ART</setSpec> <setSpec>subject:sdv</setSpec> <setSpec>subject:math</setSpec> <setSpec>collection:CNRS</setSpec> <setSpec>collection:INSMI</setSpec> <setSpec>collection:INSERM</setSpec> <setSpec>collection:UR1-SDV</setSpec> <setSpec>collection:UNIV-UBS</setSpec> <setSpec>collection:INSTITUT-TELECOM</setSpec> <setSpec>collection:IRISA_SET</setSpec> <setSpec>collection:IRSET</setSpec> <setSpec>collection:UNIV-RENNES1</setSpec> <setSpec>collection:INRIA</setSpec> <setSpec>collection:IRSET-SMLF</setSpec> <setSpec>collection:IRISA</setSpec> <setSpec>collection:INRIA_TEST</setSpec> <setSpec>collection:INRIA2</setSpec> <setSpec>collection:CENTRALESUPELEC</setSpec> <setSpec>collection:BIOSIT</setSpec> <setSpec>collection:UR1-HAL</setSpec> <setSpec>collection:UR1-UFR-SVE</setSpec> <setSpec>collection:UR1-MATH-STIC</setSpec> <setSpec>collection:UNIV-AG</setSpec> <setSpec>collection:IFR140</setSpec> <setSpec>collection:EHESP</setSpec> <setSpec>collection:USPC</setSpec> <setSpec>collection:UR1-UFR-ISTIC</setSpec> <setSpec>collection:UNIV-ANGERS</setSpec> <setSpec>collection:IRSET-5</setSpec> <setSpec>collection:DIMNP</setSpec> <setSpec>collection:BS</setSpec> <setSpec>collection:UNIV-MONTPELLIER</setSpec> </header> <metadata><dc> <publisher>HAL CCSD</publisher> <title lang=en>Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors</title> <creator>Swarup Samal, Satya</creator> <creator>Naldi, Aurélien</creator> <creator>Grigoriev, Dima</creator> <creator>Weber, Andreas</creator> <creator>Théret, Nathalie</creator> <creator>Radulescu, Ovidiu</creator> <contributor>Bonn-Aachen International Center for Information Technology (B-IT) ; RWTH Aachen University - University of Applied Sciences Bonn-Rhein-Sieg - Fraunhofer Gesellschaft - University of Bonn</contributor> <contributor>Dynamique des interactions membranaires normales et pathologiques (DIMNP) ; Université Montpellier 1 (UM1) - Université Montpellier 2 - Sciences et Techniques (UM2) - Université de Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS)</contributor> <contributor>Laboratoire Paul Painlevé - UMR 8524 (LPP) ; Université de Lille, Sciences et Technologies - Centre National de la Recherche Scientifique (CNRS)</contributor> <contributor> Institut für Informatik II [Bonn] ; Bonn Universität [Bonn]</contributor> <contributor>Institut de recherche, santé, environnement et travail [Rennes] (Irset) ; Université d'Angers (UA) - Université des Antilles et de la Guyane (UAG) - Université de Rennes 1 (UR1) - École des Hautes Études en Santé Publique [EHESP] (EHESP) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )</contributor> <contributor>Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss) ; Inria Rennes – Bretagne Atlantique ; Institut National de Recherche en Informatique et en Automatique (Inria) - Institut National de Recherche en Informatique et en Automatique (Inria) - GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7) ; Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA) ; CentraleSupélec - Université de Rennes 1 (UR1) - Télécom Bretagne - Institut National des Sciences Appliquées (INSA) - Institut National de Recherche en Informatique et en Automatique (Inria) - École normale supérieure - Rennes (ENS Rennes) - Centre National de la Recherche Scientifique (CNRS) - Université de Bretagne Sud (UBS) - CentraleSupélec - Université de Rennes 1 (UR1) - Télécom Bretagne - Institut National des Sciences Appliquées (INSA) - Institut National de Recherche en Informatique et en Automatique (Inria) - École normale supérieure - Rennes (ENS Rennes) - Centre National de la Recherche Scientifique (CNRS) - Université de Bretagne Sud (UBS) - Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA) ; CentraleSupélec - Université de Rennes 1 (UR1) - Télécom Bretagne - Institut National des Sciences Appliquées (INSA) - Institut National de Recherche en Informatique et en Automatique (Inria) - École normale supérieure - Rennes (ENS Rennes) - Centre National de la Recherche Scientifique (CNRS) - Université de Bretagne Sud (UBS) - CentraleSupélec - Université de Rennes 1 (UR1) - Télécom Bretagne - Institut National des Sciences Appliquées (INSA) - École normale supérieure - Rennes (ENS Rennes) - Centre National de la Recherche Scientifique (CNRS) - Université de Bretagne Sud (UBS)</contributor> <description>International audience</description> <source>ISSN: 0303-2647</source> <source>BioSystems</source> <publisher>Elsevier</publisher> <identifier>hal-01379033</identifier> <identifier>https://hal.inria.fr/hal-01379033</identifier> <identifier>https://hal.inria.fr/hal-01379033/document</identifier> <identifier>https://hal.inria.fr/hal-01379033/file/Samal_et_al_Biosystems_final.pdf</identifier> <source>https://hal.inria.fr/hal-01379033</source> <source>BioSystems, Elsevier, 2016, 149, pp.3-14. 〈10.1016/j.biosystems.2016.07.004〉</source> <identifier>DOI : 10.1016/j.biosystems.2016.07.004</identifier> <relation>info:eu-repo/semantics/altIdentifier/doi/10.1016/j.biosystems.2016.07.004</relation> <identifier>PUBMED : 27452668</identifier> <relation>info:eu-repo/semantics/altIdentifier/pmid/27452668</relation> <language>en</language> <subject lang=en>Tropical Geometry</subject> <subject lang=en>Cancer Systems Biology</subject> <subject lang=en>Finite State Automaton</subject> <subject lang=en>Metastability</subject> <subject>[SDV] Life Sciences [q-bio]</subject> <subject>[MATH] Mathematics [math]</subject> <type>info:eu-repo/semantics/article</type> <type>Journal articles</type> <description lang=en>We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is much slower compared to the rest of the phase space. These metastable regimes depend on the network topology and on the orders of magnitude of the kinetic parameters. Benchmarking of the method on a computational biology model repository suggests that the number of metastable regimes is sub-exponential in the number of variables and equations. The dynamics of the network can be described as a sequence of jumps from one metastable regime to another. We show that a geometrically computed con-nectivity graph restricts the set of possible jumps. We also provide finite state machine (Markov chain) models for such dynamic changes. Applied to signal transduction models, our approach unravels dynamical and functional * corresponding author capacities of signalling pathways, as well as parameters responsible for speci-ficity of the pathway response. In particular, for a model of TGFβ signalling, we find that the ratio of TGFBR2 to TGFBR1 receptors concentrations can be used to discriminate between metastable regimes. Using expression data from the NCI60 panel of human tumor cell lines, we show that aggressive and non-aggressive tumour cell lines function in different metastable regimes and can be distinguished by measuring the relative concentrations of receptors of the two types.</description> <date>2016-07-11</date> </dc> </metadata> </record> </GetRecord> </OAI-PMH>