BIOINFORMATICS ALGORITHMS Techniques and applications

Bioinformatics,broadlydefinedastheinterfacebetweenbiologicalandcomputational
sciences,isarapidlyevolvingfield,drivenbyadvancesinhighthroughputtechnolo-
giesthatresultinaneverincreasingvarietyandvolumeofexperimentaldatatobe
managed,integrated,andanalyzed.Atthecoreofmanyoftherecentdevelopmentsin
thefieldarenovelalgorithmictechniquesthatpromisetoprovidetheanswerstokey
challengesinpostgenomicbiomedicalsciences,fromunderstandingmechanismsof
genomeevolutionanduncoveringthestructureofregulatoryandprotein-interaction
networkstodeterminingthegeneticbasisofdiseasesusceptibilityandelucidationof
historicalpatternsofpopulationmigration.
Thisbookaimstoprovideanin-depthsurveyofthemostimportantdevelop-
mentsinbioinformaticsalgorithmsinthepostgenomicera.Itisneitherintendedas
anintroductorytextinbioinformaticsalgorithmsnorasacomprehensivereviewof
themanyactiveareasofbioinformaticsresearch—toreadersinterestedinthesewe
recommendtheexcellenttextbook AnIntroductiontoBioinformaticsAlgorithms by
JonesandPevznerandthe HandbookofComputationalMolecularBiology edited
bySrinivasAluru.Rather,ourintentionistomakeacarefullyselectedsetofad-
vancedalgorithmictechniquesaccessibletoabroadreadership,includinggraduate
studentsinbioinformaticsandrelatedareasandbiomedicalprofessionalswhowant
toexpandtheirrepertoireofalgorithmictechniques.Wehopethatouremphasison
bothin-depthpresentationoftheoreticalunderpinningsandapplicationstocurrent
biomedicalproblemswillbestpreparethereadersfordevelopingtheirownextensions
tothesetechniquesandforsuccessfullyapplyingtheminnewcontexts.
Thebookfeatures21chaptersauthoredbyrenownedbioinformaticsexpertswho
areactivecontributorstotherespectivesubjects.Thechaptersareintendedtobe
largelyindependent,sothatreadersdonothavetoreadeverychapternorhavetoread
theminaparticularorder.Theopeningchapterisathoughtprovokingdiscussionof
therolethatalgorithmsshouldplayin21stcenturybioinformaticseducation.The
remaining20chaptersaregroupedintothefollowingfiveparts:
PartIfocusesonalgorithmictechniquesthatfindapplicationstoawiderangeof
bioinformaticsproblems,includingchaptersondynamicprogramming,graph-
theoreticalmethods,hiddenMarkovmodels,sortingthefastFouriertransform,
seeding,andphylogeneticnetworkscomparisonapproximationalgorithms.
PartIIisdevotedtoalgorithmsandtoolsforgenomeandsequenceanalysis.
Itincludeschaptersonformalandapproximatemodelsforgeneclusters,and
onadvancedalgorithmsformultipleandnon-overlappinglocalalignmentsand
genomethings,multiplexPCRprimersetselection,andsequenceandnetwork
motiffinding.
PartIIIconcentratesonalgorithmsformicroarraydesignanddataanalysis.
Thefirstchapterisdevotedtoalgorithmsformicroarraylayout,withnexttwo
chaptersdescribingmethodsformissingvalueimputationandmeta-analysis
ofgeneexpressiondata.
PartIVexploresalgorithmicissuesarisinginanalysisofgeneticvariationacross
humanpopulation.Twochaptersaredevotedtocomputationalinferenceof
haplotypesfromcommonlyavailablegenotypedata,withathirdchapter
describingoptimizationtechniquesfordiseaseassociationsearchinepidemi-
ologiccase/controlgenotypedatastudies.
PartVgivesanoverviewofalgorithmicapproachesinstructuralandsystemsbi-
ology.Firsttwochaptersgiveaformalintroductiontotopologicalandstructural
classificationinbiochemistry,whilethethirdchaptersurveysprotein–protein
anddomain–domaininteractionprediction.
Wearegratefultoalltheauthorsfortheirexcellentcontributions,withoutwhich
thisbookwouldnothavebeenpossible.Wehopethattheirdeepinsightsandfresh
enthusiasmwillhelpattractingnewgenerationsofresearcherstothisdynamicfield.
WewouldalsoliketothankserieseditorsYiPanandAlbertY.Zomayafornurturing
thisprojectsinceitsinception,andtheeditorialstaffatWileyIntersciencefortheir
patienceandassistancethroughouttheproject.Finally,wewishtothankourfriends
andfamiliesfortheircontinuoussupport.
Ion I.M˘ andoiuand AlexanderZelikovsky