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[null,"1.","Record Nr.",null,"UNIPARTHENOPE000005364"]
[null,null,"Autore",null,"Ridolfi, Pierluigi"]
[null,null,"Titolo",null,"Firma elettronica: tecniche, norme, applicazioni / Pierluigi Ridolfi"]
[null,null,"Pubbl/distr/stampa",null,"Milano : FrancoAngeli, c2003"]
[null,null,"ISBN",null,"88-464-4178-8"]
[null,null,"Descrizione fisica",null,"239 p. ; 23 cm"]
[null,null,"Disciplina",null,"005.82"]
[null,null,"Collocazione",null,"005 -F /1"]
[null,null,"Lingua di pubblicazione",null,"Italiano"]
[null,null,"Formato",null,"Materiale a stampa"]
[null,null,null,"Livello bibliografico","Monografia"]
[null,"2.","Record Nr.",null,"UNINA9910143879403321"]
[null,null,"Titolo",null,"Computational Methods in Systems Biology : First International Workshop, CMSB 2003, Roverto, Italy, February 24–26, 2003 / / edited by Corrado Priami"]
[null,null,"Pubbl/distr/stampa",null,"Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2003"]
[null,null,"ISBN",null,"3-540-36481-1"]
[null,null,"Edizione",null,"[1st ed. 2003.]"]
[null,null,"Descrizione fisica",null,"1 online resource (IX, 214 p.)"]
[null,null,"Collana",null,"Lecture Notes in Computer Science, , 0302-9743 ; ; 2602"]
[null,null,"Disciplina",null,"572.8/0285"]
[null,null,"Soggetti",null,"Life sciences"]
[{"$nulls":4},"Computers"]
[{"$nulls":4},"Algorithms"]
[{"$nulls":4},"Logic, Symbolic and mathematical"]
[{"$nulls":4},"Computer simulation"]
[{"$nulls":4},"Bioinformatics"]
[{"$nulls":4},"Life Sciences, general"]
[{"$nulls":4},"Computation by Abstract Devices"]
[{"$nulls":4},"Algorithm Analysis and Problem Complexity"]
[{"$nulls":4},"Mathematical Logic and Formal Languages"]
[{"$nulls":4},"Simulation and Modeling"]
[null,null,"Lingua di pubblicazione",null,"Inglese"]
[null,null,"Formato",null,"Materiale a stampa"]
[null,null,null,"Livello bibliografico","Monografia"]
[null,null,null,"Note generali","Bibliographic Level Mode of Issuance: Monograph"]
[null,null,null,"Nota di bibliografia","Includes bibliographical references at the end of each chapters and index."]
[null,null,"Nota di contenuto",null,"Invited Papers -- Cells as Computation -- Formal Modeling of C. elegans Development: A Scenario-Based Approach -- Regular Papers -- Causal ?-Calculus for Biochemical Modelling -- Graphs for Core Molecular Biology -- Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa -- Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing -- Multiscale Modeling of Alternative Splicing Regulation -- A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information -- Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data -- Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach -- Mathematical Modeling of the Influence of RKIP on the ERK "]
[{"$nulls":4},"Signaling Pathway -- A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli -- Symbolic Model Checking of Biochemical Networks -- Presentation Abstracts -- Coupled Oscillator Models for a Set of Communicating Cells -- Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude -- A Core Modeling Language for the Working Molecular Biologist (Abstract) -- Integrating Simulation Packages via Systems Biology Mark-Up Language -- Recreating Biopathway Databases towards Simulation -- How to Synthesize an Optimized Genetic ?-Switching System? A System-Theoretic Approach Based on SQP -- Simulation Sudy of the TNF? Mediated NF-?B Signaling Pathway -- Detection and Analysis of Unexpected State Components in Biological Systems -- Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis -- An Overview of Data Models for the Analysis of Biochemical Pathways -- Discrete Event Systems and Client-Server Model for Signaling Mechanisms -- Position Papers -- Enhanced Operational Semantics in Systems Biology -- Issues in Computational Methods for Functional Genomics and Systems Biology -- Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics (Position Paper) -- Computer Simulation of Protocells -- How to Solve Semantic Puzzles of Systems Biology -- Evolution as Design Engineer -- Inference, Modeling and Simulation of Gene Networks."]
[null,null,null,"Sommario/riassunto","Molecularbiologyhasuntilnowmainlyfocussedonindividualmolecules,on theirpropertiesasisolatedentitiesorascomplexesinverysimplemodelsystems. However,biologicalmoleculesinlivingsystemsparticipateinverycomplexn- works,includingregulatorynetworksforgeneexpression,intracellularmetabolic networksandbothintra-andintercellularcommunicationnetworks. Suchn- worksareinvolvedinthemaintenance(homeostasis)aswellasthedi'erentiation ofcellularsystemsofwhichwehaveaveryincompleteunderstanding. Nevertheless,theprogressinmolecularbiologyhasmadepossiblethedetailed descriptionofthecomponentsthatconstitutelivingsystems,notablygenesand proteins. Large-scalegenomesequencingmeansthatwecan(atleastinpr- ciple)delineateallmacromolecularcomponentsofagivencellularsystem,and microarrayexperimentsaswellaslarge-scaleproteomicswillsoongiveuslarge amountsofexperimentaldataongeneregulation,molecularinteractionsand cellularnetworks. Thechallengeofthe21stcenturywillbetounderstandhow theseindividualcomponentsintegrateintocomplexsystemsandthefunction andevolutionofthesesystems,thusscalingupfrommolecularbiologytos- temsbiology. Bycombiningexperimentaldatawithadvancedformaltheories fromcomputerscience,\"theformallanguageforbiologicalsystems\"tospecify dynamicmodelsofinteractingmolecularentitieswouldbeessentialfor:(i)- derstandingthenormalbehaviourofcellularprocesses,andhowchangesmay a'ecttheprocessesandcausedisease-itmaybepossibletocorrelategenetic propertiesandsymptomsinnewandmoree'cientways,basedonanactual- derstandingofhowvariousprocessesinteract;(ii)providingpredictabilityand ?exibilitytoacademic,pharmaceutical,biotechnologyandmedicalresearchers studyinggeneorproteinfunctions. Inparticular,itmaysavetimebyreducing thenumberofexperimentsneeded,ifinadequatehypothesescanbeexcludedby computersimulation. "]
[{"$nulls":4},"Inresponsetothecallforpapers39weresubmittedtoCMSB2003. Allthe submittedpaperswerereviewedandtheprogrammecommittee(listedbelow) selected11high-qualitypapersforpublicationinthisvolume. Thecareofthe reviewersandoftheprogrammecommitteemembersinreviewingthepapers wassurelyvaluable. Afurther11paperswereselectedonlyforpresentationat theworkshopinordertostimulatediscussions(anabstractisincluded). AttheworkshopEhudShapiroandMichaelSterngavetwoinvited talks whosetopicsaredescribedinpapersincludedinthisvolume. Theprogramme committeedecidedtoacceptforpublicationinthisvolumealsosomeposition papers that highlight the research trends in this new ?eld of computational methodsinsystemsbiology. Thereasonisthatbecausethisisthe'rstedition ofaworkshopinthisfast-growing'eldalargeviewofpotentialtopicsofresearch wasconsideredextremelyimportant. Rovereto,December2002 CorradoPriami ProgrammeCommitteeofCMSB 2003 CorradoPriami(Chair),UniversityofTrento(Italy), CharlesAu'ray,CNRS,Villejuif(France), CosimaBaldari,Universit`adiSiena(Italy), AlexanderBockmayr,Universit´eHenriPoincar´e(France), LucaCardelli,MicrosoftResearchCambridge(UK), VincentDanos,Universit´eParisVII(France), PierpaoloDegano,Universitad ` iPisa(Italy), Francois ¸ Fages,INRIA,Rocquencourt(France), DrabløsFinn,NorwegianUniversityofScienceandTechnology,Trondheim(N- way), MonikaHeiner,BrandenburgUniversityofTechnologyatCottbus(Germany), InaKoch,UniversityofAppliedSciencesBerlin,(Germany), JohnE. Ladbury,UniversityCollegeLondon(UK), PatrickLincoln,SRI(USA), SatoruMiyano,UniversityofTokyo(Japan), GordonPlotkin,UniversityofEdinburgh(UK), SimonPlyte,PharmaciaCorporation(Italy), AvivRegev,WeizmannInstituteofScience(Israel), MagaliRoux-Rouqui´e,BSMIPasteurInstitute(France), VincentSchachter,HybrigenicsParis(France), MasaruTomita,KeioUniversity(Japan), AdelindeUhrmacher,UniversityofRostock(Germany), AlfonsoValencia,CNB-CSIC,CentroNacionaldeBiotecnologia(Spain), OlafWolkenhauer,UMIST,Manchester(UK) Local Organizing Committee Corrado Priami, Linda Brodo, Michela de Concini, Debora Schuch da Rosa Machado,andtheUniversityofTrentoEventsandMeetingsO'ce. List ofReferees F. Abascal,N. Chabrier,A. Cimatti,M. Curti,M. D. Devignes,S. Gnesi, J. Guijarro,K. Hafez,E. Klipp,C. Laneve,P. LopezRomero,F. Luccio, R. Marangoni,M. Padron,M. C. Pinotti,R. Rizzi,S. Tini. Acknowledgement TheworkshopwassponsoredandpartiallysupportedbytheUniversityofTrento, ComunediRovereto,APT,andtheEUprojectIST-32072-DEGAS. Table of Contents IInvitedPapers CellsasComputation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 AmitaiRegevandEhudShapiro FormalModelingofC. elegansDevelopment:AScenario-BasedApproach . . . 4 Na''aman Kam,David Harel,Hillel Kugler, RamiMarelly, AmirPnueli, E. JaneAlbertHubbard, andMichael J. Stern IIRegularPapers Causal?-CalculusforBiochemicalModelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Michele Curti,Pierpaolo Degano, andCosima Tatiana Baldari GraphsforCoreMolecularBiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Vincent Danos and Cosimo Laneve ContributionofComputationalTreeLogic toBiologicalRegulatoryNetworks: ExamplefromPseudomonasAeruginosa. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 SabinePeresandJean-PaulComet ModelingCellularBehaviorwithHybridAutomata: BisimulationandCollapsing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, andMarta Simeoni MultiscaleModelingofAlternativeSplicingRegulation. . . . . . . . . . . . . . . . . "]
[{"$nulls":4},". . . . 75 Damien Eveillard, Delphine Ropers,Hidde deJong,Christiane Branlant, andAlexanderBockmayr AMethodforEstimatingMetabolicFluxes fromIncompleteIsotopomerInformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 JuhoRousu,AriRantanen,HannuMaaheimo, Esa Pitk¨ anen, KatjaSaarela, andEsko Ukkonen DynamicBayesianNetworkandNonparametricRegression forNonlinearModelingofGeneNetworks fromTimeSeriesGeneExpressionData. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 SunYongKim, SeiyaImoto, andSatoru Miyano VIII Table ofContents DiscreteEventSimulationforaBetterUnderstanding ofMetaboliteChanneling-ASystemTheoreticApproach. . . . . . . . . . . . . . . . 114 Daniela Degenring,Mathias Rohl, ¨ andAdelinde M. Uhrmacher MathematicalModelingoftheIn'uenceofRKIP ontheERKSignalingPathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Kwang-HyunCho, Sung-YoungShin, Hyun-WooKim,Olaf Wolkenhauer, Brian McFerran,and WalterKolch AMethodtoIdentifyEssentialEnzymesintheMetabolism: ApplicationtoEscherichia Coli. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."]