Computational Methods in Cell Biology PDF
Preview Computational Methods in Cell Biology
Methods in Cell Biology VOLUME 110 Computational Methods in Cell Biology Series Editors Leslie Wilson DepartmentofMolecular,CellularandDevelopmentalBiology UniversityofCalifornia SantaBarbara,California Paul Matsudaira DepartmentofBiologicalSciences NationalUniversityofSingapore Singapore Methods in Cell Biology VOLUME 110 Computational Methods in Cell Biology Edited by Anand R. Asthagiri DepartmentofChemicalEngineering,NortheasternUniversity,Boston,MA,USA Adam P. Arkin DepartmentofBioengineering,UniversityofCalifornia,Berkeley,CA,USA AMSTERDAM (cid:1) BOSTON (cid:1) HEIDELBERG (cid:1) LONDON NEWYORK (cid:1) OXFORD (cid:1) PARIS (cid:1) SANDIEGO SANFRANCISCO (cid:1) SINGAPORE (cid:1) SYDNEY (cid:1) TOKYO AcademicPressisanimprintofElsevier AcademicPressisanimprintofElsevier 225WymanStreet,Waltham,MA02451,USA 525BStreet,Suite1900,SanDiego,CA92101-4495,USA 32,JamestownRoad,LondonNW17BY,UK LinacreHouse,JordanHill,OxfordOX28DP,UK Firstedition2012 Copyright#2012ElsevierInc.Allrightsreserved Nopartofthispublicationmaybereproduced,storedinaretrievalsystem ortransmittedinanyformorbyanymeanselectronic,mechanical,photocopying, recordingorotherwisewithoutthepriorwrittenpermissionofthepublisher PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRights DepartmentinOxford,UK:phone(+44)(0)1865843830;fax(+44)(0)1865853333; email:permissions@elsevier.com.Alternativelyyoucansubmityourrequestonlineby visitingtheElsevierwebsiteathttp://elsevier.com/locate/permissions,andselecting ObtainingpermissiontouseElseviermaterial Notice Noresponsibilityisassumedbythepublisherforanyinjuryand/ordamagetopersons orpropertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseor operationofanymethods,products,instructionsorideascontainedinthematerialherein. Becauseofrapidadvancesinthemedicalsciences,inparticular,independentverification ofdiagnosesanddrugdosagesshouldbemade ISBN:978-0-12-388403-9 ISSN:0091-679X For information on all Academic Press publications visitourwebsiteatelsevierdirect.com PrintedandboundinUSA 121314 10987654321 CONTRIBUTORS Numbers in parentheses indicate the pages on which the author’s contributions begin. Mark Alber (367), Department of Applied and Computational Mathematics, University of Notre Dame, Notre Dame, Indiana, USA; Department of Medicine,IndianaUniversitySchoolofMedicine,Indianapolis,Indiana,USA Alphan Altinok (285), Division of Biology, California Institute of Technology, Pasadena,California,USA AnilAswani(243),DepartmentofElectricalEngineeringandComputerSciences, UniversityofCalifornia,Berkeley,California,USA JulioM.Belmonte(325),DepartmentofPhysics,BiocomplexityInstitute,Indiana University,Bloomington,Indiana,USA Peter Bickel (243), Department of Statistics, University of California, Berkeley, California,USA Mark D. Biggin (243, 263), Genomics Division, Lawrence Berkeley National Laboratory,Berkeley,California,USA RichardBonneau(19),DepartmentofBiology,CenterforGenomicsandSystems Biology, New York University, New York, NY, USA; Computer Science Department,CourantInstituteofMathematicalSciences,NewYork,NY,USA Joseph P. Califano (139), Department of Biomedical Engineering, Cornell University,Ithaca,NewYork,USA ShawnP.Carey(139),DepartmentofBiomedicalEngineering,CornellUniversity, Ithaca,NewYork,USA Scott Christley (367), Department of Surgery, University of Chicago, Chicago, Illinois,USA Ann E. Cowan (195), R. D. Berlin Center for Cell Analysis and Modeling, UniversityofConnecticutHeathCenter,Farmington,CT,USA Alexandre Cunha (285), Center for Advanced Computing Research, Division of Engineering andAppliedScience, CaliforniaInstituteofTechnology,Pasadena, California, USA; Center for Integrative Study of Cell Regulation, California InstituteofTechnology,Pasadena,California,USA Hana El-Samad (111), Department of Biochemistry and Biophysics, California InstituteforQuantitativeBiosciences,UniversityofCalifornia,SanFrancisco,CA Ernest Fraenkel (57), Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge,Massachusetts,USA xi xii Contributors Ambhighainath Ganesan (1), Department of Biomedical Engineering, Johns HopkinsUniversity,Baltimore,Maryland,USA James A. Glazier (325), Department of Physics, BiocomplexityInstitute, Indiana University,Bloomington,Indiana,USA Alex Greenfield (19), Computational Biology Program, New York University SchoolofMedicine,NewYork,NY,USA CameronHarvey(367),DepartmentofPhysics,UniversityofNotreDame,Notre Dame,Indiana,USA Jason M. Haugh (223), Department of Chemical and Biomolecular Engineering, NorthCarolinaStateUniversity,Raleigh,NorthCarolina,USA DimitrijHmeljak(325),DepartmentofPhysics,BiocomplexityInstitute,Indiana University,Bloomington,Indiana,USA Alexander Hoffmann (81), Signaling Systems Laboratory, San Diego Center for Systems Biology of Cellular Stress Responses, Program in Bioinformatics and SystemsBiology,UniversityofCaliforniaSanDiego,LaJolla,California,USA Shao-shanCarolHuang(57),DepartmentofBiologicalEngineering,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Current address: Plant MolecularandCellularBiologyLaboratory,SalkInstitutefor BiologicalStudies, LaJolla,California,USA Tommy Kaplan (263), Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, USA; School of Computer Science and Engineering, The Hebrew University,Jerusalem,Israel Oleg Kim (367), Department of Applied and Computational Mathematics, UniversityofNotreDame,NotreDame,Indiana,USA Casey M. Kraning-Rush (139), Department of Biomedical Engineering, Cornell University,Ithaca,NewYork,USA Andre Levchenko (1), Department of Biomedical Engineering, Johns Hopkins University,Baltimore,Maryland,USA Joshua Lioi (367), Department of Applied and Computational Mathematics and Statistics,UniversityofNotreDame,NotreDame,Indiana,USA Leslie M. Loew (195), R. D. Berlin Center for Cell Analysis and Modeling, UniversityofConnecticutHeathCenter,Farmington,CT,USA Paul M. Loriaux (81), Signaling Systems Laboratory, San Diego Center for Systems Biology of Cellular Stress Responses, Program in Bioinformatics and SystemsBiology,UniversityofCaliforniaSanDiego,LaJolla,California,USA ElliotM.Meyerowitz(285),DivisionofBiology,CaliforniaInstituteofTechnology, Pasadena,California,USA EricMjolsness(285),DepartmentofComputerScience,UniversityofCalifornia, Irvine,California,USA IonI.Moraru(195),R.D.BerlinCenterforCellAnalysisandModeling,University ofConnecticutHeathCenter,Farmington,CT,USA Contributors xiii RobertF.Murphy(179),LaneCenterforComputationalBiology,CarnegieMellon University, Pittsburgh, Pennsylvania, USA; Freiburg Institute for Advanced Studies,UniversityofFreiburg,Freiburg,Germany Christopher S. Poultney (19), Department of Biology, Center for Genomics and SystemsBiology,NewYorkUniversity,NewYork,NY,USA CynthiaA.Reinhart-King(139),DepartmentofBiomedicalEngineering,Cornell University,Ithaca,NewYork,USA Adrienne H.K. Roeder (285), Center for Integrative Study of Cell Regulation, California Institute of Technology, Pasadena, California, USA; Division of Biology,CaliforniaInstituteofTechnology,Pasadena,California,USA Elliot D. Rosen (367), Department of Medical and Molecular Genetics, Indiana UniversitySchoolofMedicine,Indianapolis,Indiana,USA James C. Schaff (195), R. D. Berlin Center for Cell Analysis and Modeling, UniversityofConnecticutHeathCenter,Farmington,CT,USA AbbasShirinifard(325),DepartmentofPhysics,BiocomplexityInstitute,Indiana University,Bloomington,Indiana,USA Boris M. Slepchenko (195), R. D. Berlin Center for Cell Analysis and Modeling, UniversityofConnecticutHeathCenter,Farmington,CT,USA Jacob Stewart-Ornstein (111), Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco,CA Wenzhao Sun (367), Department of Applied and Computational Mathematics, UniversityofNotreDame,NotreDame,Indiana,USA Maciej H. Swat (325), Department of Physics, Biocomplexity Institute, Indiana University,Bloomington,Indiana,USA Paul T. Tarr (285), Division of Biology, California Institute of Technology, Pasadena,California,USA Gilberto L. Thomas (325), Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, Indiana, USA; Instituto de F(cid:1)ısica, UniversidadeFederaldoRioGrandedoSul,C.P.15051,PortoAlegre,Brazil ClaireTomlin(243),DepartmentofElectricalEngineeringandComputerSciences, UniversityofCalifornia,Berkeley,California,USA ErikS.Welf(223),DepartmentofChemicalandBiomolecularEngineering,North CarolinaStateUniversity,Raleigh,NorthCarolina,USA Zhiliang Xu (367), Department of Applied and Computational Mathematics, UniversityofNotreDame,NotreDame,Indiana,USA PREFACE Computation is an essential part of the cell biologist’s toolbox. The value of computationinanalyzingsystemsinvolvingnumerous,interconnectedmechanisms haslongbeenappreciated.Computationalmodelsprovideaframeworknotonlyto formallyrepresentandsimulatethemechanisms,butalsopredicttheresponseofan integrated system to new perturbations and thereby lead to testable hypotheses. In this way, computational modeling and analysis can suggest new experiments that challengeandhelpreviseourmechanisticunderstandingofthecellsystem. Prediction and hypothesis-generation, however, tells only part of the story. The needforcomputationisnowfarmorepervasiveincellbiology.Cellbiologicaldata isincreasinglygatheredwithhighbandwidth,oftenexploitingheterotypicmeasure- ment modalities. This flood of data includes changes in gene expression, post- translational modifications, and the subcellular location of key regulatory events. The ‘-omic’scale in vivo imaging of spatiotemporal patterns in gene expression during the development of model organisms is a compelling example. Extracting meaningfuldatafromsuchimagesisakeychallengeandinvolvesreliablesegmen- tation,annotation,storageanddatamanagement,bioinformatics,anddatamining. Havingacquiredthedata,oneseekstoinfersalientmechanisticrelationshipsand models.Derivingamodelofhowasystemworksbasedonexperimentaldatais,of course,notnew.Thechallengenowisthatthevolume,thespatiotemporalresolution, andtheheterotypicnatureofthedatamakesuchinferencesdifficulttoexecuteby intuitionalone.Computationalalgorithmstosiftthroughthedataandextractmodels consistent with the data are essential. Furthermore, model schematics, whether derivedbycomputationorintuition,areconceptual untiltheyareusedtogenerate concrete,testablepredictions.Makingsuchpredictions,however,isencumberedby a dearth of information regarding parameter values and by the fact that cellular mechanisms often operate over multiple time and spatial scales, in many cases combiningbiochemicalandmechanicalelements.Thus,inferringcomputablemod- els that are amenable to simulation requires inference not onlyof the mechanistic connections,butalsotheparametersthatdescribethestrengthofthoseconnections andinteractions. Thisremarkablebreadthofapplicationsofcomputationincellbiologyimpresses thefactthatcomputationismorethanamoduleinamulti-stepprocessthatinvolves iterativefeedbackbetweenmodelandexperiment.Itisalsoincreasinglyintegralto howdataisgatheredandinterpreted,howmechanisticmodelsareinferred,andhow newmechanismsarehypothesizedanduncovered.Thisvolumecapturesthisbroad integrationofcomputationinexperimentalcellbiology.Thevolumecoverstherole ofcomputationintheextractionofquantitativeinformationfromrawdata;inference xv xvi Preface of mechanistic computable (i.e., parameterized) models from large, heterotypic datasets;andpredictionandhypothesis-generationtodrivenewexperiments. Thecontributorstothisvolumewerepresentedwithadifficultchallenge:totailor each chapter in a way that provides both high-level and in-depth tutorials of key computational methods, while also communicating the biological question that inspiredthecomputationalapproachandthebiologicalinsightsthatwereuncovered. The contributors have, in our opinion, succeeded admirably in tackling this chal- lenge. The chapters are organized into three parts that focus on (1) molecular regulatory networks, (2) spatial and biophysical aspects of cell regulation, and finally (3) multicellular systems. Each part of the volume contains chapters that dealwith the different applications of computation in cell biology: measurements anddataextraction,modeldevelopmentandinference,andpredictionandhypoth- esisgeneration. With acknowledgment and deepest gratitude to the tremendous efforts of the contributorsandtothemanyanonymouspeer reviewers,wearepleasedtopresent thisvolumeandtrustthatitwillprovideinspirationandinstructivetutorialinyour searchfortherightcomputationaltoolforyourcellbiologyquest. AnandR.Asthagiri DepartmentofChemicalEngineering, NortheasternUniversity,Boston, Massachusetts,USA AdamP.Arkin DepartmentofBioengineering, UniversityofCalifornia,Berkeley, California,USA September30,2011 CHAPTER 1 Principles of Model Building: An Experimentation-Aided Approach to Development of Models for Signaling Networks Ambhighainath Ganesan and Andre Levchenko DepartmentofBiomedicalEngineering,JohnsHopkinsUniversity,Baltimore,Maryland,USA Abstract I. Introduction II. SignalingSystemsandMathematicalModels III. Experimentation-aidedModelDevelopment A. TemplateIdentification B. ModuleDevelopment C. ArchitecturalRevision D. ModelSimulations IV. Conclusion Acknowledgments References Abstract Livingcellscontinuouslyprobetheirenvironmentandrespondtoamultitudeof external cues. The information about the environment is carried by signaling cas- cades that act as ‘‘internal transducing and computing modules,’’ coupled into complexandinterconnectednetworks.Acomprehensiveunderstandingofhowcells makedecisionsthereforenecessitatesasoundtheoreticalframework,whichcanbe achievedthroughmathematicalmodelingofthesignalingnetworks.Inthischapter, we conceptually describe the typicalworkflow involved in building mathematical modelsthat are motivated by and are developed in a tight integration with experi- mentalanalysis.Inparticular,wedelineatethestepsinvolvedinageneric,iterative experimentation-driven model-building process, both through informal discussion METHODSINCELLBIOLOGY,VOL110 0091-679X/10$35.00 Copyright2012,ElsevierInc.Allrightsreserved. 1 DOI10.1016/B978-0-12-388403-9.00001-1
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