Foundations of Systems Biology

290 Pages·2001·3.615 MB·English

by  Hiroaki Kitano

Foundations of Systems Biology
edited by
Hiroaki Kitano
TheMITPress
Cambridge,Massachusetts
London,England
(cid:1)c 2001MassachusettsInstituteofTechnology
Allrightsreserved.Nopartofthisbookmaybereproducedinanyformbyanyelectronicor
mechanicalmeans(includingphotocopying,recording,orinformationstorageandretrieval)
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ThisbookwassetinPalatinobytheauthorusingtheLATEXdocumentpreparationsystem.
PrintedonrecycledpaperandboundintheUnitedStatesofAmerica.
LibraryofCongressCataloging-in-PublicationData
Foundationsofsystemsbiology
editedbyHiroakiKitano.-1sted.
p.cm.
Includedbibliographicalreferences(p.).
ISBN0-262-11266-3(hc.:alk.paper)
1.Biologicalsystems-Research-Methodology
2.Biologicalsystems-Research-Casestudies.
I.Kitano,Hiroaki,1961-
QH313.F662002
573-dc21
2001042807
Contents
Contributors ix
Preface xiii
1 Systems Biology: Toward System-level
UnderstandingofBiologicalSystems 1
HiroakiKitano
I ADVANCEDMEASUREMENTSYSTEMS
2 AutomaticAcquisition of Cell Lineage through
4DMicroscopy andAnalysisof EarlyC.elegans
Embryogenesis 39
ShuichiOnami,ShugoHamahashi,MasaoNagasaki,
SatoruMiyano,andHiroakiKitano
II REVERSE ENGINEERING AND DATA MINING FROM GENE
EXPRESSIONDATA
3 TheDBRFMethodforInferringaGeneNetwork
fromLarge-ScaleSteady-StateGeneExpressionData 59
ShuichiOnami,KojiM.Kyoda,MineoMorohashi,and
HiroakiKitano
4 TheAnalysisofCancerAssociatedGeneExpression
Matrices 77
MattiasWahdeandZoltanSzallasi
5 Automated Reverse Engineering of Metabolic
PathwaysfromObservedDatabyMeansofGenetic
Programming 95
JohnR.Koza,WilliamMydlowec,GuidoLanza,Jessen
Yu,andMartinA.Keane
III SOFTWAREFORMODELINGANDSIMULATION
6 The ERATO Systems Biology Workbench: An
Integrated Environment for Multiscale and
MultitheoreticSimulationsinSystemsBiology 125
Michael Hucka, Andrew Finney, Herbert Sauro,
HamidBolouri,JohnDoyle,andHiroakiKitano
7 Automatic Model Generation for Signal
Transduction withApplications to MAP-Kinase
Pathways 145
Bruce E. Shapiro, Andre Levchenko, and Eric
Mjolsness
8 ModelingLargeBiologicalSystemsFromFunctional
GenomicData:ParameterEstimation 163
PedroMendes
IV CELLULARSIMULATION
9 TowardsaVirtualBiologicalLaboratory 189
Jo¨rgStelling,AndreasKremling,MartinGinkel,Katja
BettenbrockandErnstDieterGilles
10 Computational Cell Biology — The Stochastic
Approach 213
ThomasSimonShimizuandDennisBray
11 Computer Simulation of the Cell: Human
ErythrocyteModelanditsApplication 233
YoichiNakayamaandMasaruTomita
V SYSTEM-LEVELANALYSIS
12 ConstructingMathematicalModelsofBiological
Signal Transduction Pathways: An Analysis of
Robustness 251
Tau-MuYi
13 Combination of Biphasic Response Regulation
and PositiveFeedback as a GeneralRegulatory
MechanisminHomeostasisandSignalTransduction 263
Andre Levchenko, Jehoshua Bruck, and Paul W.
Sternberg
14 DistinctRolesofRho-kinasePathwayandMyosin
LightChainKinasePathwayinPhosphorylationof
MyosinLightChain:KineticSimulationStudy 279
Shinya Kuroda, Nicolas Schweighofer, Mutsuki
Amano,KozoKaibuchi,andMitsuoKawato
vi Contents
Contributors
MutsukiAmano and
DivisionofSignalTransduction, ControlandDynamicalSystems,
NaraInstituteofScienceand CaliforniaInstituteofTechnology.
Technology.
AndrewFinney
KatjaBettenbrock
aJSfTin/[email protected]
[email protected] BiologyProject,
DynamicsofComplexTechnical and
Systems. ControlandDynamicalSystems,
CaliforniaInstituteofTechnology.
HamidBolouri
ErnstDieterGilles
hJSbTol/[email protected]
BiologyProject, [email protected]
and DynamicsofComplexTechnical
ControlandDynamicalSystems, Systems.
CaliforniaInstituteofTechnology,
and
MartinGinkel
DivisionofBiology,
CaliforniaInstituteofTechnology,
[email protected]
and
DynamicsofComplexTechnical
ScienceandTechnologyResearch
Systems.
Centre,
UniversityofHertfordshire.
ShugoHamahashi
DennisBray
[email protected],
ERATO,JST,
[email protected],
and
UniversityofCambridge.
DepartmentofComputerScience,
KeioUniversity.
JehoshuaBruck
MichaelHucka
[email protected]
AppliedScience,
mJShTuc/[email protected]
CaliforniaInstituteofTechnology.
BiologyProject,
and
JohnDoyle ControlandDynamicalSystems,
[email protected],
ERATO,JST,
CaliforniaInstituteofTechnology. DynamicsofComplexTechnical
Systems.
KozoKaibuchi
DivisionofSignalTransduction, ShinyaKuroda
NaraInstituteofScienceand
Technology, [email protected],
and ERATO,JST,
DepartmentofCellPharmacology, and
NagoyaUniversity. DivisionofSignalTransduction,
NaraInstituteofScienceand
Technology,
MitsuoKawato
Presentaddress:Centerfor
KawatoDynamicBrainProject,
NeurobiologyandBehavior,
ERATO,JST,
ColumbiaUniversity.
and
HumanInformationProcessing
ResearchLaboratories, KojiM.Kyoda
ATR.
[email protected],
ERATO,JST,
MartinA.Keane
and
DepartmentofFundamental
[email protected]
ScienceandTechnology,
KeioUniversity.
HiroakiKitano
GuidoLanza
[email protected],
ERATO,JST,
[email protected] ingInc.
and
TheSystemsBiologyInstitute,
and AndreLevchenko
ControlandDynamicalSystems,
CaliforniaInstituteofTechnology, [email protected]
and AppliedScience,
SonyComputerScience CaliforniaInstituteofTechnology.
Laboratories,Inc.
PedroMendes
JohnR.Koza
[email protected],
[email protected],
VirginiaPolytechnicInstituteand
DepartmentofMedicine,
StateUniversity.
DepartmentofElectrical
Engineering,
StanfordUniversity. SatoruMiyano
[email protected],
AndreasKremling
ERATO,JST,
and
[email protected] HumanGenomeCenter,Institute
ofMedicalScience,
UniversityofTokyo.
x Contributors
ControlandDynamicalSystems,
CaliforniaInstituteofTechnology.
EricMjolsness
HerbertSauro
[email protected],
CaliforniaInstituteofTechnology, hJSsTau/[email protected]
and BiologyProject,
DivisionofBiology, and
CaliforniaInstituteofTechnology, ControlandDynamicalSystems,
and CaliforniaInstituteofTechnology.
KitanoSymbioticSystemsProject,
ERATO,JST.
NicolasSchweighofer
KawatoDynamicBrainProject,
MineoMorohashi ERATO,JST,
Presentaddress:LearningCurve.
[email protected],
ERATO,JST,
and BruceShapiro
DepartmentofFundamental
ScienceandTechnology, [email protected],
KeioUniversity. CaliforniaInstituteofTechnology.
WilliamMydlowec ThomasSimonShimizu
[email protected]. [email protected],
UniversityofCambridge.
MasaoNagasaki
Jo¨rgStelling
[email protected],
ERATO,JST, [email protected]
and DynamicsofComplexTechnical
DepartmentofInformation Systems.
Science,
HumanGenomeCenter,Institute
PaulW.Sternberg
ofMedicalScience,
UniversityofTokyo. [email protected]
HowardHughesMedicalInstitute,
YoichiNakayama CaliforniaInstituteofTechnology.
[email protected],
ZoltanSzallasi
KeioUniversity.
[email protected],
ShuichiOnami UniformedServicesUniversityof
theHealthSciences.
[email protected],
ERATO,JST,
MasaruTomita
and
TheSystemsBiologyInstitute, [email protected],
and
xi Contributors
KeioUniversity.
MattiasWahde
[email protected],
ChalmersUniversityof
Technology.
Tau-MuYi
[email protected],
ERATO,JST,
and
DivisionofBiology,
CaliforniaInstituteofTechnology.
JessenYu
[email protected].
xii Contributors
Preface
Systemsbiologyaimsatunderstandingbiologicalsystemsatsystemlevel.
Itisagrowingareainbiology,duetoprogressinseveralfields.Themost
critical factor has been rapid progress in molecular biology, furthered
by technologies for making comprehensive measurements on DNA se-
quence, gene expression profiles, protein-protein interactions, etc. With
the ever-increasing flow of biological data, serious attempts to under-
standbiologicalsystemsassystemsarenowalmostfeasible.Handlingthis
high-throughput experimental data places major demands on computer
science, including database processing, modeling, simulation, and anal-
ysis. Dramatic progress in semiconductor technologies has led to high-
performancecomputingfacilitiesthatcansupportsystem-levelanalysis.
This is not the first attempt at system-level analysis; there have been
severaleffortsinthepast,themostnotableofwhichiscybernetics,orbio-
logicalcybernetics,proposedbyNorbertWienermorethan30yearsago.
With the limited understanding of biological processes at the molecular
level at that time, most of the work was on phenomenological analysis
ofphysiologicalprocesses.Therehavealsobeenbiochemicalapproaches,
suchasmetaboliccontrolanalysis,andalthoughrestrictedtosteady-state
flow,ithassuccessfullybeenusedtoexploresystem-levelpropertiesofbi-
ologicalmetabolism.Systemsbiology,justlikeallotheremergingscientific
disciplines,isbuiltonmultipleeffortsthatsharethevision.However,sys-
temsbiologyisdistinctfrompastattemptsbecauseforthefirsttimeweare
able to understand biology at the system level based on molecular-level
understanding,andtocreateaconsistentsystemofknowledgegrounded
inthemolecularlevel.Inaddition,itshouldbenotedthatsystemsbiology
is intended to be biology for system-level studies, not physics, systems
science,orinformatics,whichtrytoapplycertaindogmaticprinciplesto
biology.
Whenthefieldhasmaturedinthenextfewyears,systemsbiologywill
be characterized as a field of biology at the system level with extensive
useof cutting-edge technologies andhighly automatedhigh-throughput
precisionmeasurementcombinedwithsophisticatedcomputationaltools
and analysis. Systems biology clearly includes both experimental and
computational or analytical studies. However, systems biology is not a
merecombinationofmolecularbiologyandcomputingsciencetoreverse