Computational systems biology: inference and modelling

182 Pages·2016·15.191 MB·English

by  Lecca, Paola

COMPUTATIONAL
SYSTEMS BIOLOGY
This page intentionally left blank
Woodhead Publishing Series
in Biomedicine: Number 86
COMPUTATIONAL
SYSTEMS BIOLOGY
Inference and Modeling
PAOLALECCA
ANGELARE
ADAOHAIHEKWABA
IVANMURA
THANH-PHUONGNGUYEN
AMSTERDAM(cid:129)BOSTON(cid:129)CAMBRIDGE (cid:129)HEIDELBERG
LONDON (cid:129)NEWYORK(cid:129)OXFORD(cid:129)PARIS(cid:129)SANDIEGO
SANFRANCISCO(cid:129)SINGAPORE(cid:129)SYDNEY(cid:129)TOKYO
Woodhead Publishing is an imprint of Elsevier
WoodheadPublishingisanimprintofElsevier
TheOfficers’MessBusinessCentre,RoystonRoad,Duxford,CB224QH,UK
50HampshireStreet,5thFloor,Cambridge,MA02139,USA
TheBoulevard,LangfordLane,Kidlington,OX51GB,UK
Copyright©2016ElsevierLtd.Allrightsreserved.
Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,
electronicormechanical,includingphotocopying,recording,oranyinformationstorage
andretrievalsystem,withoutpermissioninwritingfromthepublisher.Detailsonhowto
seekpermission,furtherinformationaboutthePublisher’spermissionspoliciesandour
arrangementswithorganizationssuchastheCopyrightClearanceCenterandthe
CopyrightLicensingAgency,canbefoundatourwebsite:www.elsevier.com/permissions.
Thisbookandtheindividualcontributionscontainedinitareprotectedundercopyright
bythePublisher(otherthanasmaybenotedherein).
Notices
Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchand
experiencebroadenourunderstanding,changesinresearchmethods,professionalpractices,
ormedicaltreatmentmaybecomenecessary.
Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgein
evaluatingandusinganyinformation,methods,compounds,orexperimentsdescribed
herein.Inusingsuchinformationormethodstheyshouldbemindfuloftheirownsafety
andthesafetyofothers,includingpartiesforwhomtheyhaveaprofessionalresponsibility.
Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,or
editors,assumeanyliabilityforanyinjuryand/ordamagetopersonsorpropertyasa
matterofproductsliability,negligenceorotherwise,orfromanyuseoroperationofany
methods,products,instructions,orideascontainedinthematerialherein.
BritishLibraryCataloguingin PublicationData
AcataloguerecordforthisbookisavailablefromtheBritishLibrary
LibraryofCongressCataloging-in-PublicationData
AcatalogrecordforthisbookisavailablefromtheLibraryofCongress
ISBN:978-0-08-100095-3(print)
ISBN:978-0-08-100115-8(online)
ForinformationonallWoodheadPublishingpublications
visitourwebsiteathttp://www.elsevier.com/
Publisher:GlynJones
AcquisitionEditor:GlynJones
EditorialProjectManager:HarrietClayton
ProductionProjectManager:RoshmiJoy
Designer:VickyPearsonEsser
TypesetbySPiBooks
DEDICATION
To ourstudents,nulladies sinelinea.
This page intentionally left blank
CONTENTS
AbouttheAuthors ix
Preface xiii
Acknowledgments xv
1. OverviewofBiologicalNetworkInferenceandModeling
ofDynamics 1
1.1 IntroductiontoInferenceofTopologies,Causalities,andDynamicModels 2
1.2 TheData 4
2. NetworkInferenceFromSteady-StateData 13
2.1 Median-CorrectedZScores 13
2.2 MultipleRegressionMethod 16
2.3 BayesianVariableSelectionMethod 18
3. NetworkInferenceFromTime-CourseData 21
3.1 Time-Lagged-Correlation-BasedNetworkInference 22
3.2 BayesianApproaches 34
3.3 TheMethodofVariationalBayesianInference 34
4. Network-BasedConceptualizationofObservationalData 47
4.1 BiologicalNetworkData,Sampling,andPredictability 48
4.2 CharacteristicsofBiologicalNetworks 50
4.3 ModuleDiscoveryApproaches 53
4.4 CategorizationofNetworkInferenceMethods 55
4.5 PerformanceofNetworkInferenceMethods 58
4.6 ComparisonofNetworkInferenceMethods 60
4.7 ApplicationsofNetwork-BasedDataIntegration 64
5. DeterministicDifferentialEquations 67
5.1 TheRationaleofDeterministicModeling 68
5.2 ModelingElementalandAbstractBiologicalPhenomena 74
5.3 AnalysisofDeterministicDifferentialModels 82
5.4 CaseStudies 92
6. StochasticDifferentialEquations 99
6.1 ReactionKinetics:TheMolecularApproachtoKinetics 99
6.2 StochasticDifferentialEquations 110
vii
viii Contents
7. FromNetworkInferencetotheStudyofHumanDiseases 119
7.1 IntroductiontoNetworkMedicine 120
7.2 DatabasesandToolsforNetworkMedicine 124
7.3 ACaseStudyofNeurodegenerativeDiseases 124
7.4 ConclusionandPerspectives 140
8. Conclusions 141
8.1 NetworkInference,Modeling,andSimulationintheEraofBigData
andHigh-ThroughputExperiments 141
Bibliography 145
Index 161
ABOUT THE AUTHORS
Dr. Paola Lecca received an MS degree in theoretical physics from
the University of Trento (Italy) in 1997 and a PhD degree in computer
science from the International Doctorate School in Information and
Communication Technologies of the University of Trento in 2006. Since
1998shehasheldresearcherandprincipalinvestigatorpositionsinresearch
centers and in academia. From 1998 to 2000 she was a research assistant
at the Fondazione Bruno Kessler Center for Information Technologies of
Trento in the Predictive Models for Biomedicine and the Environment
researchunit.From2001to2002sheworkedintheDepartmentofPhysics
of the University of Trento in the area of data manipulationand predictive
modelinginresearchprogramsoftheNationalInstituteofNuclearPhysics,
Italy. In 2006 she joined the Microsoft Research and University of Trento
CentreforComputationalandSystemsBiology(COSBI),Italy.AtCOSBI
sheledtheDataManipulationandKnowledgeInferenceGroup.From2012
to 2015 she continued her research at the Laboratory of Computational
OncologyoftheCentreforIntegrativeBiologyoftheUniversityofTrento.
She is currently collaborating with the Department of Mathematics of the
University of Trento, where she is developing optimized techniques for
the numerical simulation and analysis of spatial and temporal multiscale
biologicalsystems.
Paola Lecca has long experience of teaching university courses in
computer science for students of physics and simulation of biological
systems for students of computer science. She currently provides teaching
supporttothemathematicsandstatisticscourseforstudentsofbiomolecular
sciencesand technologyat the Universityof Trento.
She is a professional member of the Association for Computing
Machinery and the author of 70 publications,includingbooks and journal
and conference articles on computational biology, bioinformatics, and
biophysics.Sheisintenselyactiveasaneditorandreviewerforhigh-impact-
factor journalsin thesesubjects,and leads theorganizationof international
schoolsandsymposiain bioinformatics.
Angela Re earned her bachelor’s degree in physics in 1999 from the
University of Turin. In 2002 she completed her PhD program in complex
systems applied to postgenomic biology, which was inspired by the notion
that the breadth and depth of complexity of living systems require that
ix