Networks of Networks in Biology: Concepts, Tools and Applications

215 Pages·2021·7.598 MB·English

by  Narsis A. Kiani, David Gomez-Cabrero, Ginestra Bianconi

Networks of Networks in Biology
Concepts,ToolsandApplications
Biologicalsystemsareextremelycomplexandhaveemergentpropertiesthatcannot
be explained or even predicted by studying their individual parts in isolation. The
reductionist approach, although successful in the early days of molecular biology,
underestimates this complexity. As the amount of available data grows, so it will
become increasingly important to be able to analyse and integrate these large data
sets.Thisbookintroducesnovelapproachesandsolutionstothebigdataproblemin
biomedicine, and presents new techniques in the field of graph theory for handling
and processing multi-type large data sets. By discussing cutting-edge problems and
techniques, researchers from a wide range of fields will gain insights into how to
exploit big, heterogeneous data in the life sciences through the concept of ‘network
ofnetworks’.
Narsis A. Kiani is Assistant Professor and Co-leader of Algorithmic Dynamics in
the Department of Oncology-Pathology of the Karolinska Institutet, Sweden. She is
passionateaboutmathematicsandisinterestedinthefundamentalquestionofwhat
observationsabout effects at the microscopic level can tell us about the macroscopic
natureofbiologicalsystemsandviceversa,andhowdefectsanddisorderaffectthese
systems.
David Gomez-Cabrero is the Head of the Translational Bioinformatics Unit at
Navarrabiomed, Spain. Since 2009, he has specialized in bioinformatics and data
integrationanalysis,firstasapost-doctorateandsubsequentlyasAssistantProfessor
attheKarolinskaInstitutet,Sweden,andasSeniorLectureratKing’sCollegeLondon,
UK.Hecollaborateswithclinicalgroupsthatinvestigatemultiplesclerosis,rheuma-
toidarthritis,chronicobstructivepulmonarydisease(COPD)andcancer,amongother
diseases.
GinestraBianconiisProfessorofAppliedMathematicsatQueenMaryUniversityof
London and a Turing Fellow at The Alan Turing Institute. She is Editor-in-Chief of
theJournalofPhysics:ComplexityandEditorofScientificReportsandPLoSOne.Shehas
publishedmorethan150articlesinnetworktheoryandinterdisciplinaryapplications,
andistheauthorofthebookMultilayerNetworks:StructureandFunction.

Networks of
Networks in Biology
Concepts, Tools and Applications
Editedby
NARSIS A. KIANI
KarolinskaInstitutet,Stockholm
DAVID GOMEZ-CABRERO
King’sCollegeLondon
GINESTRA BIANCONI
QueenMaryUniversityofLondon
TheAlanTuringInstitute
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ItfurtherstheUniversity’smissionbydisseminatingknowledgeinthepursuitof
education,learning,andresearchatthehighestinternationallevelsofexcellence.
www.cambridge.org
Informationonthistitle:www.cambridge.org/9781108428873
DOI:10.1017/9781108553711
©CambridgeUniversityPress2021
Thispublicationisincopyright.Subjecttostatutoryexception
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noreproductionofanypartmaytakeplacewithoutthewritten
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Firstpublished2021
PrintedintheUnitedKingdombyTJBooksLimited,PadstowCornwall
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ISBN978-1-108-42887-3Hardback
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Contents
ListofContributors page vii
Preface ix
PartI NetworksinBiology 1
1 AnIntroductiontoBiologicalNetworks 3
NuriaPlanell,XabierMartinezdeMorentinandDavidGomez-Cabrero
2 GraphTheory 18
AkramDehnokhalajiandNasimNasrabadi
PartII NetworkAnalysis 33
3 StructuralAnalysisofBiologicalNetworks 35
NarsisA.KianiandMikkoKivela¨
4 NetworksfromanInformation-TheoreticandAlgorithmic
ComplexityPerspective 56
HectorZenilandNarsisA.Kiani
5 IntegrationandFeatureIdentificationinMulti-layerNetworksusingaHeat
DiffusionApproach 71
GordonBallandJesperTegne´r
PartIII Multi-layerNetworks 83
6 MultiplexNetworks 85
GinestraBianconi
7 ExistingToolsforAnalysisofMulti-layerNetworks 105
MassimoStellaandManlioDeDomenico
8 DynamicsonMulti-layerNetworks 121
ManlioDeDomenicoandMassimoStella
PartIV Applications 145
9 TheNetworkofNetworksInvolvedinHumanDisease 147
CelineSinandJo¨rgMenche
10 TowardsaMulti-layerNetworkAnalysisofDisease:Challengesand
OpportunitiesThroughtheLensofMultipleSclerosis 172
JesperTegne´r,IngridKockum,MikaGustafssonand
DavidGomez-Cabrero
v
vi CONTENTS
11 Microbiome:AMulti-layerNetworkViewisRequired 183
RodrigoBacigalupe,SaeedShoaieandDavidGomez-Cabrero
PartV Conclusion 195
12 ConcludingRemarks:OpenQuestionsandChallenges 197
GinestraBianconi,DavidGomez-Cabrero,JesperTegne´r
andNarsisA.Kiani
Index 201
Contributors
RodrigoBacigalupeVIB-KULeuvenCenterforMicrobiology,CampusGasthuisberg,
RegaInstituut,Leuven,Belgium
GordonBallUnitofComputationalMedicine,DepartmentofMedicineSolna,Center
forMolecularMedicine,KarolinskaInstitutet,Stockholm,Sweden(formermember)
GinestraBianconiSchoolofMathematicalSciences,QueenMaryUniversityofLon-
don,London,UK;TheAlanTuringInstitute,London,UK
AkramDehnokhalajiOperationsandInformationManagementDepartment,Aston
BusinessSchool,Birmingham,UK
ManlioDeDomenicoFondazioneBrunoKessler,Povo,Italy
DavidGomez-CabreroTranslationalBioinformaticsUnit,Navarrabiomed,Complejo
Hospitalario de Navarra (CHN), Universidad Pu´blica de Navarra (UPNA), IdiSNA,
Pamplona, Spain; Mucosal and Salivary Biology Division, King’s College London
DentalInstitute,London,UK;UnitofComputationalMedicine,CenterforMolecular
Medicine,DepartmentofMedicineSolna,KarolinskaInstitutet,KarolinskaUniversity
HospitalandScienceforLifeLaboratory,Stockholm,Sweden
MikaGustafssonDepartmentofPhysics,ChemistryandBiology(IFM)Bioinformat-
ics(BION),Linko¨pingUniversity,Linko¨ping,Sweden
NarsisA.KianiAlgorithmicDynamicsLab,UnitofComputationalMedicine,Depart-
mentofOncology-Pathology,CentreforMolecularMedicine,KarolinskaInstituteand
SciLifeLab,Stockholm,Sweden;AlgorithmicNatureGroup,LABORESfortheNatural
andDigitalSciences,Paris,France
MikkoKivela¨ DepartmentofComputerScience,SchoolofScience,AaltoUniversity,
Finland
Ingrid Kockum Department of Clinical Neuroscience and Center for Molecular
Medicine,KarolinskaInstitute,KarolinskaUniversityHospital,Stockholm,Sweden
Xabier Martinez de Morentin Translational Bioinformatics Unit, Navarrabiomed,
ComplejoHospitalariodeNavarra(CHN),UniversidadPu´blicadeNavarra(UPNA),
IdiSNA,Pamplona,Spain
Jo¨rgMencheCeMMResearchCenterforMolecularMedicineoftheAustrianAcademy
ofSciences,Vienna,Austria
NasimNasrabadiDepartmentofMathematics,UniversityofBirjand,Iran
Nuria Planell Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospi-
talario de Navarra (CHN), Universidad Pu´blica de Navarra (UPNA), IdiSNA, Pam-
plona,Spain
vii
viii LIST OF CONTRIBUTORS
SaeedShoaieCentreforHost–MicrobiomeInteractions,FacultyofDentistry,Oral&
Craniofacial Sciences, King’s College London, London, UK; Science for Life Labora-
tory,KTH–RoyalInstituteofTechnology,Stockholm,Sweden
CelineSinCeMMResearchCenterforMolecularMedicineoftheAustrianAcademy
ofSciences,Vienna,Austria
MassimoStellaFondazioneBrunoKessler,Povo,Italy
JesperTegne´rBiologicalandEnvironmentalSciencesandEngineeringDivision,Com-
puter,ElectricalandMathematicalSciencesandEngineeringDivision,KingAbdullah
UniversityofScienceandTechnology(KAUST),Thuwal,SaudiArabia;UnitofCom-
putationalMedicine,CenterforMolecularMedicine,DepartmentofMedicineSolna,
KarolinskaInstitutet,KarolinskaUniversityHospitalandScienceforLifeLaboratory,
Stockholm,Sweden
HectorZenilAlgorithmicDynamicsLab,DepartmentofOncology-Pathology,Centre
forMolecularMedicine,KarolinskaInstitute,Stockholm,Sweden;AlgorithmicNature
Group,LABORESfortheNaturalandDigitalSciences,Paris,France
Preface
NetworkScienceistransformingresearchindifferentareasoflivingsciences,ranging
from evolutionary biologyto medicine.Thisbook aimstointroducethemostrecent
developments of Network Science and its biological applications. In particular, the
architecture of biological systems will be characterized using both single networks
(monoplexes) and networks of networks (multi-layer networks). Graph theory and
social network analysis are classic subjects of mathematics and sociology that have
beenwidelyinvestigatedinthetwentiethcentury.However,onlysincethelate1990s,
whenseveralpapersonthefundamentaldesignprinciplesofvariouskindsoflarge-
scale networks were published, was Network Science established as a novel frame-
worktoanalyseinteractingsystems,whichledtotheexpansionoftheresearchfield
ofnetworkanalysis,withgreatimpactinbiology.
After20years,thisfieldisstillproliferating,andithasbecomeincreasinglyclear
thatthechallengeofintegratingandmodellingheterogeneityandcomplexityofliving
systemscannotbeaddressedbyusingasingle-layernetwork(monoplex).
Instead,thecomplexityoflivingsystems–suchastheinteractionsbetweenpro-
teins and the microbiome – is captured by a multi-layer network approach. Multi-
layernetworksareformedbynodesandinteractionsofdifferentnatures,andconno-
tations, forming different networks that interact with each other, creating a network
ofnetworks.Theinvestigationofmulti-layernetworksisaveryactiveresearcharea
inNetworkScience,whichinthelasttenyearshasledtothedevelopmentofseveral
methodologiestoextractinformationforanalysinglargedatasetsandintegratingthe
resultsfromdifferentexperiments.
With contributions from key leaders, this book discusses topics in Network Sci-
ence that are increasingly foundational for the quantitative understanding of living
systems.Furthermore,itconsolidatesexistingpracticalandtheoreticalknowledgeof
bothmonoplexesandmulti-layernetworks.Thebookbalancesapplicationandtheory
togive a unified overview of thisinterdisciplinary science.It is intendedto serve as
an introductory text for graduate students and researchers in physics, biology, and
biochemistry,andpresentsideasandtechniquesfromfieldsoutsidethereader’sown
areaofspecialization.
Aims of this Book
Thisbookfocusesonnetwork-inspiredapproachesfortheanalysisandintegrationof
thelargedatasetscurrentlyprevalentinlifesciences.Theprincipalaimofthiswork
is to give a comprehensive overview of new techniques in the field of graph theory
forhandlingandprocessingmulti-typelargedatasets.Bydiscussingstate-of-the-art
problemsandtechniques,thisbookoffersresearchersfromawiderangeofareasthe
uniqueopportunitytogaininsightsforexploitingtherichnessoflifesciencesdatasets
through the concept of ’networks of networks’. It presents a timely, multi-authored
compendium representing a diverse set of backgrounds and methods developed in
ix