Computational Methods in Systems Biology: 19th International Conference, CMSB 2021, Bordeaux, France, September 22–24, 2021, Proceedings PDF
Preview Computational Methods in Systems Biology: 19th International Conference, CMSB 2021, Bordeaux, France, September 22–24, 2021, Proceedings
Eugenio Cinquemani Loïc Paulevé (Eds.) 1 8 8 Computational Methods 2 1 I B in Systems Biology N L 19th International Conference, CMSB 2021 Bordeaux, France, September 22–24, 2021 Proceedings 123 Lecture Notes in Bioinformatics 12881 Subseries of Lecture Notes in Computer Science SeriesEditors SorinIstrail BrownUniversity,Providence,RI,USA PavelPevzner UniversityofCalifornia,SanDiego,CA,USA MichaelWaterman UniversityofSouthernCalifornia,LosAngeles,CA,USA EditorialBoardMembers SørenBrunak TechnicalUniversityofDenmark,KongensLyngby,Denmark MikhailS.Gelfand IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia ThomasLengauer MaxPlanckInstituteforInformatics,Saarbrücken,Germany SatoruMiyano UniversityofTokyo,Tokyo,Japan EugeneMyers MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,Germany Marie-FranceSagot UniversitéLyon1,Villeurbanne,France DavidSankoff UniversityofOttawa,Ottawa,Canada RonShamir TelAvivUniversity,RamatAviv,TelAviv,Israel TerrySpeed WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia MartinVingron MaxPlanckInstituteforMolecularGenetics,Berlin,Germany W.EricWong UniversityofTexasatDallas,Richardson,TX,USA Moreinformationaboutthissubseriesathttp://www.springer.com/series/5381 · Eugenio Cinquemani Loïc Paulevé (Eds.) Computational Methods in Systems Biology 19th International Conference, CMSB 2021 Bordeaux, France, September 22–24, 2021 Proceedings Editors EugenioCinquemani LoïcPaulevé Univ.GrenobleAlpes,Inria Univ.Bordeaux,BordeauxINP,CNRS, Grenoble,France LaBRI,UMR5800 Talence,France ISSN 0302-9743 ISSN 1611-3349 (electronic) LectureNotesinBioinformatics ISBN 978-3-030-85632-8 ISBN 978-3-030-85633-5 (eBook) https://doi.org/10.1007/978-3-030-85633-5 LNCSSublibrary:SL8–Bioinformatics ©SpringerNatureSwitzerlandAG2021 Chapters 9, 11 and 18 are licensed under the terms of the Creative Commons Attribution 4.0 Interna- tionalLicense(http://creativecommons.org/licenses/by/4.0/).Forfurtherdetailsseelicenseinformationin thechapters. Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow knownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookare believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaimsin publishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface This volume contains the papers presented at CMSB 2021, the 19th Interna- tional Conference on Computational Methods in Systems Biology, held during September 22–24, 2021 in a hybrid format, allowing for in-person participation in Bordeaux,France,andforonlineparticipation. TheCMSBannualconferenceseries,initiatedin2003,providesauniquediscussion forum for computer scientists, biologists, mathematicians, engineers, and physicists interestedinasystem-levelunderstandingofbiologicalprocesses.Topicscoveredbythe CMSBproceedingsincludeformalismsformodelingbiologicalprocesses;frameworks formodelverification,validation,analysis,andsimulationofbiologicalsystems;high- performancecomputationalsystemsbiology;modelinferencefromexperimentaldata; multi-scale modeling and analysis methods; computational approaches for synthetic biology; machine learning and data-driven approaches; microbial ecology modeling andanalysis;methodsandprotocolscopingwithpopulationsandtheirvariability;and models,applications,andcasestudiesinsystemsandsyntheticbiology. Therewereatotalof54submissionsoverthe4conferencetracks(regularpapers,tool papers,highlightpresentationproposals,andposters).Everyregularpaperwasreviewed byatleastthreeProgramCommitteemembers,whereaseverytoolpaperwasreviewed bytwoProgramCommitteemembersandtwoToolEvaluationCommitteemembers.The lattercommitteeprovidedathoroughevaluationofthetoolquality,intermsofusability, accessibility,reproducibility,anddocumentation.Thecommitteedecidedtoaccept13 ofthe25submittedregularpapersand5ofthe7submittedtoolpapersforpublication in this volume and presentation. The conference also included 4 of the 7 proposed highlight presentations and 16 posters not included in the proceedings. The program of CMSB was further enriched by five notorious invited speakers: Diego di Bernardo (TIGEM,Italy),LaurenceCalzone(InstitutCurie,Paris),GiuliaGiodano(Universityof Trento,Italy),Yang-YuLiu(HarvardMedicalSchool,USA),andIonPetre(Universityof Turku,Finland).AdditionalinformationaboutCMSB2021isavailableontheconference websiteathttps://cmsb2021.labri.fr. WearedeeplygratefultothemembersoftheProgramCommittee,ToolEvaluation Committee,andtheexternalreviewersfortheirinvaluablecontributiontothereviewing process and the feedback they provided to the authors. Special thanks go to Auriane Dantès and Isabelle Garcia for taking care of the administrative aspects of the local organization, to Clémence Frioux, Misbah Razzaq, and Laurent Simon for their help inscientificandpracticalorganizationalmatters,toSamuelPastvaaschairoftheTool EvaluationCommittee,andtoFrançoisFagesandallthemembersoftheCMSBSteering Committee, for their advice on the organization and the running of the conference. WethankEasyChairforthesupportofferedbyitsconferencesysteminthereviewing processandtheproductionoftheseproceedings,andSpringerforpublishingtheCMSB proceedings in its Lecture Notes in Computer Science series. Finally, we are grateful totheLaboratoireBordelaisdeRechercheenInformatique(LaBRI)forsupportingand hostingCMSB2021,aswellastoCNRS,UniversitédeBordeauxanditsDépartement vi Preface Santépublique,BordeauxINP,Inria,ANR,andtheSysNumclusterofexcellence,for theirfinancialsupport. Last but not least, we immensely thank all authors, speakers, and contributors for makingCMSBafirst-classscientificevent. September2021 EugenioCinquemani LoïcPaulevé Organization ProgramCommittee EugenioCinquemani(Co-chair) Inria,France LoïcPaulevé(Co-chair) CNRS/LaBRI,Bordeaux,France AlessandroAbate UniversityofOxford,UK ClaudioAltafini LinköpingUniversity,Sweden PaoloBallarini CentraleSupelec,France EzioBartocci TUWien,Austria LucaBortolussi UniversityofTrieste,Italy LucaCardelli UniversityofOxford,UK MilanCeska BrnoUniversityofTechnology,CzechRepublic NeilDalchau Microsoft,USA FrançoisFages Inria,France KarolineFaust KULeuven,Belgium JeromeFeret Inria,France ChristophFlamm UniversityofVienna,Austria ClémenceFrioux Inria,France AshutoshGupta TIFR,India JanHasenauer UniversityofBonn,Germany MonikaHeiner BrandenburgTechnicalUniversity Cottbus-Senftenberg,Germany JaneHillston TheUniversityofEdinburgh,UK InaKoch Johann Wolfgang Goethe University Frankfurt am Main,Germany JanKretinsky TechnicalUniversityofMunich,Germany JeanKrivine CNRS,France PedroT.Monteiro INESC-ID/IST-UniversidadedeLisboa,Portugal LauraNenzi UniversityofTrieste,Italy JunPang UniversityofLuxembourg,Luxembourg NicolaPaoletti RoyalHolloway,UniversityofLondon,UK IonPetre UniversityofTurku,Finland TatjanaPetrov UniversityofKonstanz,Germany CarlaPiazza UniversityofUdine,Italy OvidiuRadulescu UniversityofMontpellier2,France AndreRibeiro TampereUniversity,Finland MariaRodriguezMartinez IBM,ZurichResearchLaboratory,Switzerland OlivierRoux LS2N,ÉcoleCentraledeNantes,France GuidoSanguinetti TheUniversityofEdinburgh,UK HeikeSiebert DFG Research Center Matheon, Freie Universität Berlin,Germany AbhyudaiSingh UniversityofDelaware,USA viii Organization ScottSmolka StonyBrookUniverstiy,USA CarolynTalcott SRIInternational,USA AdelindeUhrmacher UniversitätRostock,Germany AndreaVandin Sant’AnnaSchoolofAdvancedStudies,Pisa,Italy VerenaWolf SaarlandUniversity,Germany ChristophZechner MaxPlanckInstituteofMolecularCellBiologyand Genetics,Germany DavidŠafránek MasarykUniversity,CzechRepublic ToolEvaluation Committee SamuelPastva(Chair) MasarykUniversity,CzechRepublic GeorgiosArgyris TechnicalUniversityofDenmark,Copenhagen, Denmark CandanÇelik ComeniusUniversityinBratislava,Slovakia LauraCifuentesFontanals Freie Universität Berlin/Max Planck Institute for MolecularGenetics,Germany AurélienDesoeuvres UniversityofMontpellier,France LukréciaMertová MasarykUniversity,LaboratorySYBILA, CzechRepublic GarethMolyneux UniversityofOxford,UK LoïcPaulevé CNRS/LaBRI,Bordeaux,France MisbahRazzaq EcoleCentraledeNantes,France Organization Committee AurianeDantès CNRS,LaBRI,France ClémenceFrioux Inria,France IsabelleGarcia CNRS,LaBRI,France MisbahRazzaq InsermBPH,Bordeaux,France LaurentSimon BordeauxINP,LaBRI,France SteeringCommittee AlessandroAbate(Guest) UniversityofOxford,UK LucaBortolussi(Guest) UniversityofTrieste,Italy LucaCardelli UniversityofOxford,UK EugenioCinquemani(Guest) InriaGrenoble-Rhône-Alpes,France FinnDrablos NTNU,Norway FrançoisFages InriaSaclayîle-de-France,France DavidHarel WeizmannInstituteofScience,Israel MonikaHeiner BrandenburgTechnicalUniversity Cottbus-Senftenberg,Germany Organization ix TommasoMazza IRCCSCasaSollievodellaSofferenzaMendel, Italy SatoruMiyano UniversityofTokyo,Japan LoïcPaulevé(Guest) CNRS,LaBRI,France IonPetre UniversityofTurku,Finland TatjanaPetrov(Guest) UniversityofKonstanz,Germany GordonPlotkin TheUniversityofEdinburgh,UK CorradoPriami CoSBi/Microsoft Research, University of Trento, Italy GuidoSanguinetti(Guest) TheUniversityofEdinburgh,UK CarolynTalcott SRIInternational,USA AdelindeUhrmacher UniversityofRostock,Germany VerenaWolf SaarlandUniversity,Germany AdditionalReviewers Ackermann,Jörg Mizera,Andrzej Backeköhler,Michael Molyneux,Gareth Cairoli,Francesca Piho,Paul Gilbert,David Regolin,Enrico Klarner,Hannes Krüger,Thilo Sinzger,Mark Labarthe,Simon Tonello,Elisa
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