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Bioinformatics
Bioinformatics
Editedby AndreasD.Baxevanis,GaryD.Bader,andDavidS.Wishart
FourthEdition
Thisfourtheditionfirstpublished2020 ©2020JohnWiley&Sons,Inc.
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LibraryofCongressCataloging-in-PublicationData
Names:Baxevanis,AndreasD.,editor.|Bader,GaryD.,editor.|Wishart, DavidS.,editor.
Title:Bioinformatics/editedbyAndreasD.Baxevanis,GaryD.Bader,DavidS. Wishart.
Othertitles:Bioinformatics(Baxevanis)
Description:Fourthedition.|Hoboken,NJ:Wiley,2020.|Includes bibliographicalreferencesandindex.
Identifiers:LCCN2019030489(print)|ISBN9781119335580(cloth)|ISBN 9781119335962(adobepdf)|ISBN9781119335955(epub)
Subjects:MESH:ComputationalBiology–methods|SequenceAnalysis–methods |BaseSequence|Databases,NucleicAcid|Databases,Protein Classification:LCCQH324.2(print)|LCCQH324.2(ebook)|NLMQU 550.5.S4|DDC570.285–dc23
LCrecordavailableathttps://lccn.loc.gov/2019030489
LCebookrecordavailableathttps://lccn.loc.gov/2019030490
CoverDesign:Wiley
CoverImages:©DavidWishart,background©Suebsiri/GettyImages
Setin9.5/12.5ptSTIXTwoTextbySPiGlobal,Chennai,India
10987654321
Contents
Foreword vii
Preface ix
Contributors xi
AbouttheCompanionWebsite xvii
1BiologicalSequenceDatabases 1 AndreasD.Baxevanis
2InformationRetrievalfromBiologicalDatabases 19 AndreasD.Baxevanis
3AssessingPairwiseSequenceSimilarity:BLASTandFASTA 45 AndreasD.Baxevanis
4GenomeBrowsers 79 TyraG.Wolfsberg
5GenomeAnnotation 117 DavidS.Wishart
6PredictiveMethodsUsingRNASequences 155 MichaelF.Sloma,MichaelZuker,andDavidH.Mathews
7PredictiveMethodsUsingProteinSequences 185 JonasReeb,TatyanaGoldberg,YanayOfran,andBurkhardRost
8MultipleSequenceAlignments 227 FabianSievers,GeoffreyJ.Barton,andDesmondG.Higgins
9MolecularEvolutionandPhylogeneticAnalysis 251 EmmaJ.GriffithsandFionaS.L.Brinkman
10ExpressionAnalysis 279 MariekeL.Kuijjer,JosephN.Paulson,andJohnQuackenbush
11ProteomicsandProteinIdentificationbyMassSpectrometry 315 SadhnaPhanseandAndrewEmili
12ProteinStructurePredictionandAnalysis 363 DavidS.Wishart
13BiologicalNetworksandPathways 399 GaryD.Bader
14Metabolomics 437
DavidS.Wishart
15PopulationGenetics 481
LynnB.JordeandW.ScottWatkins
16MetagenomicsandMicrobialCommunityAnalysis 505 RobertG.Beiko
17TranslationalBioinformatics 537
SeanD.MooneyandStephenJ.Mooney
18StatisticalMethodsforBiologists 555 HunterN.B.Moseley
Appendices 583
Glossary 591 Index 609
Foreword
AsIreviewthematerialpresentedinthefourtheditionof Bioinformatics Iammovedintwo ways,relatedtoboththepastandthefuture.
Lookingtothepast,Iammovedbytheamazingevolutionthathasoccurredinourfield sincethefirsteditionofthisbookappearedin1998.Twenty-oneyearsisalong,longtimein anyscientificfield,butespeciallysointheagilefieldofbioinformatics.Tousethewell-trodden metaphorofthe“biologymoonshot,”thelaunchpadatthebeginningofthetwenty-firstcenturywasthedeterminationofthehumangenome.Discoveryisnottherightwordforwhat transpired–weknewitwasthereandwhatwasneeded.Synergyisperhapsabetterword; synergyoftechnologicaldevelopment,experiment,computation,andpolicy.Atrulycollaborative efforttocontinuouslyshare,inareusableway,thecollectiveeffortsofmanyscientists. Bioinformaticswasbornfromthissynergyandhascontinuedtogrowandflourishbasedon theseprinciples.
Thatgrowthisreflectedinboththescopeanddepthofwhatiscoveredinthesepages.These attributesareareflectionoftheincreasedcomplexityofthebiologicalsystemsthatwestudy (movingfrom“simple”modelorganismstothehumancondition)andthescalesatwhich thosestudiestakeplace.Asacommunitywehaveprofessedmultiscalemodelingwithout muchtoshowforit,butitwouldseemtobefinallyhere.Wenowhavetheabilitytoconnectthe dotsfrommolecularinteractions,throughthepathwaystowhichthosemoleculesbelongto thecellstheyaffect,totheinteractionsbetweenthosecellsthroughtotheeffectstheyhaveon individualswithinapopulation.Toolsandmethodologiesthatwerenovelinearliereditions ofthisbookarenowroutineorobsolete,andnewer,faster,andmoreaccurateproceduresare nowwithus.Thiswillcontinue,andassuchthisbookprovidesavaluablesnapshotofthe scopeanddepthofthefieldasitexiststoday.
Lookingtothefuture,thisbookprovidesafoundationforwhatistocome.Formethisis afieldmoreaptlyreferredto(andperhapsanewsubtitleforthenextedition)asBiomedicalDataScience.SittingasIdonow,asDeanofaSchoolofDataSciencewhichcollaborates openlyacrossalldisciplines,Iseerapidchangeakintowhathappenedtobirthbioinformatics20ormoreyearsago.Itwillnottake20yearsforotherdisciplinestocatchup;Ipredictit willtake2!Theaccomplishmentsoutlinedinthisbookcanhelpdefinewhatotherdisciplines willaccomplishwiththeirowndataintheyearstocome.Statisticalmethods,cloudcomputing,dataanalytics,notablydeeplearning,themanagementoflargedata,visualization,ethics policy,andthelawsurroundingdataaregeneric.Bioinformaticshassomuchtooffer,yetit willalsobeinfluencedbyotherfieldsinawaythathasnothappenedbefore.Forty-fiveyears inacademiatellsmethatthereisnothingtocompareacrosscampusestowhatishappening today.Thisisbothanopportunityandathreat.Theeditorsandauthorsofthiseditionshould becomplimentedforsettingthestageforwhatistocome.
PhilipE.Bourne,UniversityofVirginia
Preface
Inputtingtogetherthistextbook,wehopethatstudentsfromarangeoffields–including biology,computerscience,engineering,physics,mathematics,andstatistics–benefitbyhavingaconvenientstartingpointforlearningmostofthecoreconceptsandmanyusefulpractical skillsinthefieldofbioinformatics,alsoknownascomputationalbiology.
Studentsinterestedinbioinformaticsoftenaskabouthowshouldtheyacquiretrainingin suchaninterdisciplinaryfieldasthisone.Inanidealworld,studentswouldbecomeexperts inallthefieldsmentionedabove,butthisisactuallynotnecessaryandrealisticallytoomuch toask.Allthatisrequiredistocombinetheirscientificinterestswithafoundationinbiology andanysinglequantitativefieldoftheirchoosing.Whilethemostcommoncombinationis tomixbiologywithcomputerscience,incrediblediscoverieshavebeenmadethroughfinding creativeintersectionswithanynumberofquantitativefields.Indeed,manyofthesequantitativefieldstypicallyoverlapagreatdeal,especiallygiventheirfoundationaluseofmathematics andcomputerprogramming.Thesenaturalrelationshipsbetweenfieldsprovidethefoundationforintegratingdiverseexpertiseandinsights,especiallywheninthecontextofperforming bioinformaticanalyses.
Whilebioinformaticsisoftenconsideredanindependentsubfieldofbiology,itislikelythat thenextgenerationofbiologistswillnotconsiderbioinformaticsasbeingseparateandwill insteadconsidergainingbioinformaticsanddatascienceskillsasnaturallyastheylearnhowto useapipette.Theywilllearnhowtoprogramacomputer,likelystartinginelementaryschool. Otherdatascienceknowledgeareas,suchasmath,statistics,machinelearning,dataprocessing,anddatavisualizationwillalsobepartofanycorecurriculum.Indeed,thechildrenofone oftheeditorsrecentlylearnedhowtoconstructbarplotsandotherdatachartsinkindergarten! ThesameeditoristeachingprogramminginR(animportantdatascienceprogramming language)toallincomingbiologygraduatestudentsathisuniversitystartingthisyear.
Asbioinformaticsanddatasciencebecomemorenaturallyintegratedinbiology,itisworth notingthatthesefieldsactivelyespouseacultureofopenscience.Thiscultureismotivatedby thinkingaboutwhywedoscienceinthefirstplace.Wemaybecuriousorlikeproblemsolving. Wecouldalsobemotivatedbythebenefitstohumanitythatscientificadvancesbring,such astangiblehealthandeconomicbenefits.Whateverthemotivatingfactor,itisclearthatthe most efficientwaytosolvehardproblemsistoworktogetherasateam,inacomplementary fashionandwithoutduplicationofeffort.Theonlywaytomakesurethisworkseffectively istoefficientlyshareknowledgeandcoordinateworkacrossdisciplinesandresearchgroups. Presentingscientificresultsinareproducibleway,suchasfreelysharingthecodeanddata underlyingtheresults,isalsocritical.Fortunately,thereareanincreasingnumberofresources thatcanhelpfacilitatethesegoals,includingthebioRxivpreprintserver,wherepaperscanbe sharedbeforetheverylongprocessofpeerreviewiscompleted;GitHub,forsharingcomputer code;anddatasciencenotebooktechnologythathelpscombinecode,figures,andtextinaway thatmakesiteasiertosharereproducibleandreusableresults.
Wehopethistextbookhelpscatalyzethistransitionofbiologytoaquantitative,data science-intensivefield.Asbiologicalresearchadvancesbecomeevermorebuiltoninterdisciplinary,open,andteamscience,progresswilldramaticallyspeedup,layingthegroundwork forfantasticnewdiscoveriesinthefuture.
x Preface
Wealsodeeplythankallofthechapterauthorsforcontributingtheirknowledgeandtime tohelpthemanyfuturereadersofthisbooklearnhowtoapplythemyriadbioinformatic techniquescoveredwithinthesepagestotheirownresearchquestions.
AndreasD.Baxevanis GaryD.Bader
DavidS.Wishart
Contributors
GaryD.Bader,PhD isaProfessoratTheDonnellyCentreattheUniversityofToronto, Toronto,Canada,andaleaderinthefieldofNetworkBiology.Garycompletedhis postdoctoralworkinChrisSander’sgroupintheComputationalBiologyCenter(cBio)at MemorialSloan-KetteringCancerCenterinNewYork.GarycompletedhisPhDinthe laboratoryofChristopherHogueintheDepartmentofBiochemistryattheUniversityof TorontoandaBScinBiochemistryatMcGillUniversityinMontreal.Dr.Baderuses molecularinteraction,pathway,and-omicsdatatogaina“causal”mechanistic understandingofnormalanddiseasephenotypes.Hislaboratorydevelopsnovel computationalapproachesthatcombinemolecularinteractionandpathwayinformation with-omicsdatatodevelopclinicallypredictivemodelsandidentifytherapeutically targetablepathways.HealsohelpsleadtheCytoscape,GeneMANIA,andPathwayCommons pathwayandnetworkanalysisprojects.
GeoffreyJ.Barton,PhD isProfessorofBioinformaticsandHeadoftheDivisionof ComputationalBiologyattheUniversityofDundeeSchoolofLifeSciences,Dundee,UK. BeforemovingtoDundeein2001,hewasHeadoftheProteinDataBankinEuropeandthe leaderoftheResearchandDevelopmentTeamattheEMBLEuropeanBioinformatics Institute(EBI).PriortojoiningEMBL-EBI,hewasHeadofGenomeInformaticsatthe WellcomeTrustCentreforHumanGenetics,UniversityofOxford,apositionheheld concurrentlywithaRoyalSocietyUniversityResearchFellowshipintheDepartmentof Biochemistry.Geoff’slongestrunningresearchinterestisusingcomputationalmethodsto studytherelationshipbetweenaprotein’ssequence,itsstructure,anditsfunction.Hisgroup hascontributedmanytoolsandtechniquesinthefieldofproteinsequenceandstructure analysisandstructureprediction.TwoofthebestknownaretheJalviewmultiplealignment visualizationandanalysisworkbench,whichisinusebyover70000groupsforresearchand teaching,andtheJPredmulti-neuralnetproteinsecondarystructurepredictionalgorithm, whichperformspredictionsonupto500000proteins/monthforusersworldwide.In additiontohisworkrelatedtoproteinsequenceandstructure,Geoffhascollaboratedon manyprojectsthatprobebiologicalprocessesusingproteomicandhigh-throughput sequencingapproaches.Geoff’sgrouphasdeepexpertiseinRNA-seqmethodsandhas recentlypublishedatwo-condition48-replicateRNA-seqstudythatisnowakeyreference workforusersofthistechnology.
AndreasD.Baxevanis,PhD istheDirectorofComputationalBiologyfortheNational InstitutesofHealth’s(NIH)IntramuralResearchProgram.HeisalsoaSeniorScientist leadingtheComputationalGenomicsUnitattheNIH’sNationalHumanGenomeResearch Institute,Bethesda,MD,USA.Hisresearchprogramiscenteredonprobingtheinterface betweengenomicsanddevelopmentalbiology,focusingonthesequencingandanalysisof invertebrategenomesthatcanyieldinsightsofrelevancetohumanhealth,particularlyinthe areasofregeneration,allorecognition,andstemcellbiology.Hisaccomplishmentshavebeen recognizedbytheBodossakiFoundation’sAcademicPrizeinMedicineandBiologyin2000,
Greece’shighestawardforyoungscientistsofGreekheritage.In2014,hewaselectedtothe JohnsHopkinsSocietyofScholars,recognizingalumniwhohaveachievedmarked distinctionintheirfieldofstudy.HewastherecipientoftheNIH’sRuthL.Kirschstein MentoringAwardin2015,inrecognitionofhiscommitmenttoscientifictraining,education, andmentoring.In2016,Dr.BaxevaniswaselectedasaSeniorMemberoftheInternational SocietyforComputationalBiologyforhissustainedcontributionstothefieldand,in2018,he waselectedasaFellowoftheAmericanAssociationfortheAdvancementofScienceforhis distinguishedcontributionstothefieldofcomparativegenomics.
RobertG.Beiko,PhD isaProfessorandAssociateDeanforResearchintheFacultyof ComputerScienceatDalhousieUniversity,Halifax,NovaScotia,Canada.HeisaformerTier IICanadaResearchChairinBioinformatics(2007–2017),anAssociateEditoratmSystems andBMCBioinformatics,andafoundingorganizeroftheCanadianBioinformatics WorkshopsinMetagenomicsandGenomicEpidemiology.Heisalsotheleadeditorofthe recentlypublishedbook MicrobiomeAnalysis intheMethodsinMolecularBiologyseries.His researchfocusesonmicrobialgenomics,evolution,andecology,withconcentrationsinthe areaoflateralgenetransferandmicrobialcommunityanalysis.
FionaS.L.Brinkman,PhD,FRSC
isaProfessorinBioinformaticsandGenomicsinthe DepartmentofMolecularBiologyandBiochemistryatSimonFraserUniversity,Vancouver, BritishColumbia,Canada,withcross-appointmentsinComputingScienceandtheFacultyof HealthSciences.Sheismostknownforherresearchanddevelopmentofwidelyused computersoftwarethataidsbothmicrobe(PSORTb,IslandViewer)andhumangenomic (InnateDB)evolutionary/genomicsanalyses,alongwithherinsightsintopathogen evolution.Sheiscurrentlyco-leadinganationaleffort–theIntegratedRapidInfectious DiseaseAnalysisProject–thegoalofwhichistousemicrobialgenomesasafingerprintto bettertrackandunderstandthespreadandevolutionofinfectiousdiseases.Shehasalso beenleadingdevelopmentintoanapproachtointegrateverydiversedatafortheCanadian CHILDStudybirthcohort,includingmicrobiome,genomic,epigenetic,environmental,and socialdata.Shecoordinatescommunity-basedgenomeannotationanddatabase developmentforresourcessuchasthePseudomonasGenomeDatabase.Shealsohasastrong interestinbioinformaticseducation,includingdevelopingthefirstundergraduatecurricula usedasthebasisforthefirstWhitePaperonCanadianBioinformaticsTrainingin2002.She isonseveralcommitteesandadvisoryboards,includingtheBoardofDirectorsforGenome Canada;shechairstheScientificAdvisoryBoardfortheEuropeanNucleotideArchive (EMBL-EBI).Shehasreceivedanumberofawards,includingaTR100awardfromMIT,and, mostrecently,wasnamedasaFellowoftheRoyalSocietyofCanada.
AndrewEmili,PhD isaProfessorintheDepartmentsofBiochemistry(MedicalSchool)and Biology(ArtsandSciences)atBostonUniversity(BU),Boston,MA,USA,andtheinaugural DirectoroftheBUCenterforNetworkSystemsBiology(CNSB).PriortoBoston,Dr.Emili wasafoundingmemberandPrincipalInvestigatorfor18yearsattheDonnellyCenterfor CellularandBiomolecularResearchattheUniversityofToronto,oneofthepremierresearch centersinintegrativemolecularbiology.Dr.Emiliisaninternationallyrecognizedleaderin functionalproteomics,systemsbiology,andprecisionmassspectrometry.Hisgroupdevelops andappliesinnovativetechnologiestosystematicallymapproteininteractionnetworksand macromolecularcomplexesofcellsandtissuesonaglobalscale,publishing“interactome” mapsofunprecedentedquality,scope,andresolution.
TatyanaGoldberg,PhD isapostdoctoralscientistattheTechnicalUniversityofMunich, Germany.SheobtainedherPhDinBioinformaticsunderthesupervisionofDr.Burkhard Rost.Herresearchfocusesondevelopingmodelsthatcanpredictthelocalizationofproteins withincells.Theresultsofherstudycontributetoavarietyofapplications,includingthe developmentofpharmaceuticalsforthetreatmentofAlzheimerdiseaseandcancer.
EmmaJ.Griffiths,PhD isaresearchassociateintheDepartmentofPathologyandLaboratory MedicineattheUniversityofBritishColumbiainVancouver,Canada,workingwithDr. WilliamHsiao.Dr.GriffithsreceivedherPhDfromtheDepartmentofBiochemistryand BiomedicalSciencesatMcMasterUniversityinHamilton,Canada,withherdoctoralwork focusingontheevolutionaryrelationshipsbetweendifferentgroupsofbacteria.Shehassince pursuedpostdoctoraltraininginthefieldsofchemicalandfungalgeneticsandmicrobial genomicswithDr.FionaBrinkmanintheDepartmentofBiochemistryandMolecular BiologyatSimonFraserUniversityinVancouver,Canada.Hercurrentworkfocusesonthe developmentofontology-drivenapplicationsdesignedtoimprovepathogengenomics contextualdata(“metadata”)exchangeduringpublichealthinvestigations.
DesmondG.Higgins,PhD isProfessorofBioinformaticsinUniversityCollegeDublin,Ireland, wherehislaboratoryworksongenomicdataanalysisandsequencealignmentalgorithms.He earnedhisdoctoraldegreeinzoologyfromTrinityCollegeDublin,Ireland,andhasworkedin thefieldofbioinformaticssince1985.HisgroupmaintainsanddevelopstheClustalpackage formultiplesequencealignmentincollaborationwithgroupsinFrance,Germany,andthe UnitedKingdom.Dr.HigginswrotethefirstversionofClustalinDublinin1988.Hethen movedtotheEMBLDataLibrarygrouplocatedinHeidelbergin1990andlatertoEMBL-EBI inHinxton.ThiscoincidedwiththereleaseofClustalWand,later,ClustalX,whichhasbeen extremelywidelyusedandcited.Currently,hehasrunoutofversionletterssoisworkingon ClustalOmega,specificallydesignedformakingextremelylargeproteinalignments.
LynnB.Jorde,PhD hasbeenonthefacultyoftheUniversityofUtahSchoolofMedicine,Salt LakeCity,UT,USA,since1979andholdstheMarkandKathieMillerPresidentialEndowed ChairinHumanGenetics.HewasappointedChairoftheDepartmentofHumanGeneticsin September2009.Dr.Jorde’slaboratoryhaspublishedscientificarticlesonhumangenetic variation,high-altitudeadaptation,thegeneticbasisofhumanlimbmalformations,andthe geneticsofcommondiseasessuchashypertension,juvenileidiopathicarthritis,and inflammatoryboweldisease.Dr.Jordeistheleadauthorof MedicalGenetics,atextbookthat isnowinitsfiftheditionandtranslatedintomultipleforeignlanguages.Heisthe co-recipientofthe2008AwardforExcellenceinEducationfromtheAmericanSocietyof HumanGenetics(ASHG).Heservedtwo3-yeartermsontheBoardofDirectorsofASHG and,in2011,hewaselectedaspresidentofASHG.In2012,hewaselectedasaFellowofthe AmericanAssociationfortheAdvancementofScience.
MariekeL.Kuijjer,PhD isaGroupLeaderattheCentreforMolecularMedicineNorway (NCMM,aNordicEMBLpartner),UniversityofOslo,Norway,wheresherunsthe ComputationalBiologyandSystemsMedicinegroup.Sheobtainedherdoctorateinthe laboratoryofDr.PancrasHogendoornintheDepartmentofPathologyattheLeiden UniversityMedicalCenterintheNetherlands.Afterthis,shecontinuedherscientific trainingasapostdoctoralresearcherinthelaboratoryofDr.JohnQuackenbushatthe Dana-FarberCancerInstituteandHarvardT.H.ChanSchoolofPublicHealth,duringwhich shewonacareerdevelopmentawardandapostdoctoralfellowship.Dr.Kuijjer’sresearch focusesonsolvingfundamentalbiologicalquestionsthroughthedevelopmentofnew methodsincomputationalandsystemsbiologyandonimplementingthesetechniquesto betterunderstandgeneregulationincancer.Dr.Kuijjerservesontheeditorialboardof CancerResearch
DavidH.Mathews,MD,PhD isaprofessorofBiochemistryandBiophysicsandalsoof BiostatisticsandComputationalBiologyattheUniversityofRochesterMedicalCenter, Rochester,NY,USA.HealsoservesastheAssociateDirectoroftheUniversityofRochester’s CenterforRNABiology.HisinvolvementineducationincludesdirectingtheBiophysicsPhD programandteachingacourseinPythonprogrammingandalgorithmsfordoctoralstudents withoutaprogrammingbackground.HisgroupstudiesRNAbiologyanddevelopsmethods
forRNAsecondarystructurepredictionandmolecularmodelingofthree-dimensional structure.HisgroupdevelopedandmaintainsRNAstructure,awidelyusedsoftwarepackage forRNAstructurepredictionandanalysis.
SeanD.Mooney,PhD hasspenthiscareerasaresearcherandgroupleaderinbiomedical informatics.HenowleadsResearchITforUWMedicineandisleadingeffortstosupportand buildclinicalresearchinformaticplatformsasitsfirstChiefResearchInformationOfficer (CRIO)andasaProfessorintheDepartmentofBiomedicalInformaticsandMedical EducationattheUniversityofWashington,Seattle,WA,USA.Previoustobeingappointedas CRIO,hewasanAssociateProfessorandDirectorofBioinformaticsattheBuckInstitutefor ResearchonAging.AsanAssistantProfessor,hewasappointedinMedicalandMolecular GeneticsatIndianaUniversitySchoolofMedicineandwasthefoundingDirectorofthe IndianaUniversitySchoolofMedicineBioinformaticsCore.In1997,hereceivedhisBSwith DistinctioninBiochemistryandMolecularBiologyfromtheUniversityofWisconsinat Madison.HereceivedhisPhDfromtheUniversityofCaliforniainSanFranciscoin2001, thenpursuedhispostdoctoralstudiesunderanAmericanCancerSocietyJohnPeter HoffmanFellowshipatStanfordUniversity.
StephenJ.Mooney,PhD isanActingAssistantProfessorintheDepartmentofEpidemiology attheUniversityofWashington,Seattle,WA,USA.HedevelopedtheCANVASsystemfor collectingdatafromGoogleStreetViewimageryasagraduatestudent,andhisresearch focusesoncontextualinfluencesonphysicalactivityandtransport-relatedinjury.He’sa methodsgeekatheart.
HunterN.B.Moseley,PhD isanAssociateProfessorintheDepartmentofMolecularand CellularBiochemistryattheUniversityofKentucky,Lexington,KY,USA.Heisalsothe InformaticsCoreDirectorwithintheResourceCenterforStableIsotopeResolved Metabolomics,AssociateDirectorfortheInstituteforBiomedicalInformatics,andamember oftheMarkeyCancerCenter.Hisresearchinterestsincludedevelopingcomputational methods,tools,andmodelsforanalyzingandinterpretingmanytypesofbiologicaland biophysicaldatathatenablenewunderstandingofbiologicalsystemsandrelateddisease processes.Hisformaleducationspansmultipledisciplinesincludingchemistry, mathematics,computerscience,andbiochemistry,withexpertiseinalgorithmdevelopment, mathematicalmodeling,structuralbioinformatics,andsystemsbiochemistry,particularlyin thedevelopmentofautomatedanalysesofnuclearmagneticresonanceandmass spectrometrydataaswellasknowledge–dataintegration.
YanayOfran,PhD isaProfessorandheadoftheLaboratoryofFunctionalGenomicsand SystemsBiologyatBarIlanUniversityinTelAviv,Israel.Hisresearchfocuseson biomolecularrecognitionanditsroleinhealthanddisease.ProfessorOfranisalsothe founderofBiolojicDesign,abiopharmaceuticalcompanythatusesartificialintelligence approachestodesignepitope-specificantibodies.Heisalsotheco-founderofUkko,a biotechnologycompanythatusescomputationaltoolstodesignsafeproteinsforthefoodand agriculturesectors.
JosephN.Paulson,PhD isaStatisticalScientistwithinGenentech’sDepartmentof Biostatistics,SanFrancisco,CA,USA,workingondesigningclinicaltrialsandbiomarker discovery.Previously,hewasaResearchFellowintheDepartmentofBiostatisticsand ComputationalBiologyattheDana-FarberCancerInstituteandDepartmentofBiostatistics attheHarvardT.H.ChanSchoolofPublicHealth.HegraduatedwithaPhDinApplied Mathematics,Statistics,andScientificComputationfromtheUniversityofMaryland, CollegeParkwherehewasaNationalScienceFoundationGraduateFellow.Asastatistician andcomputationalbiologist,hisinterestsincludeclinicaltrialdesign,biomarkerdiscovery,
developmentofcomputationalmethodsfortheanalysisofhigh-throughputsequencingdata whileaccountingfortechnicalartifacts,andthemicrobiome.
SadhnaPhanse,MSc isaBioinformaticsAnalystattheDonnellyCentreforCellularand BiomolecularResearchattheUniversityofToronto,Toronto,Canada.Shehasbeenactivein thefieldofproteomicssince2006asamemberoftheEmiliresearchgroup.Hercurrentwork involvestheuseofbioinformaticsmethodstoinvestigatebiologicalsystemsandmolecular associationnetworksinhumancellsandmodelorganisms.
JohnQuackenbush,PhD isProfessorofComputationalBiologyandBioinformaticsandChair oftheDepartmentofBiostatisticsattheHarvardT.H.ChanSchoolofPublicHealth,Boston, MA,USA.HealsoholdsappointmentsintheChanningDivisionofNetworkMedicineof BrighamandWomen’sHospitalandattheDana-FarberCancerInstitute.Heisarecognized expertincomputationalandsystemsbiologyanditsapplicationstothestudyofawiderange ofhumandiseasesandthefactorsthatdrivethosediseasesandtheirresponsestotherapy.Dr. Quackenbushhaslongbeenanadvocateforopenscienceandreproducibleresearch.Asa foundingmemberandpastpresidentoftheFunctionalGenomicsDataSociety(FGED),he wasadeveloperoftheMinimalInformationAboutaMicroarrayExperiment(MIAME)and otherdata-reportingstandards.Dr.QuackenbushwashonoredbyPresidentBarackObama in2013asaWhiteHouseOpenScienceChampionofChange.
JonasReeb,MSc isaPhDstudentinthelaboratoryofBurkhardRostattheTechnical UniversityofMunich,Germany(TUM).DuringhisstudiesatTUM,hehasworkedon predictivemethodsfortheanalysisandevaluationoftransmembraneproteins;hehasalso workedontheNYCOMPSstructuralgenomicspipeline.Hisdoctoralthesisfocusesonthe effectofsequencevariantsandtheirprediction.
BurkhardRost,PhD isaprofessorandAlexandervonHumboldtAwardrecipientatthe TechnicalUniversityofMunich,Germany(TUM).Hewasthefirsttocombinemachine learningwithevolutionaryinformation,usingthiscombinationtoaccuratelypredict secondarystructure.Sincethattime,hisgrouphasrepeatedthissuccessindevelopingmany othertoolsthatareactivelyusedtopredictandunderstandaspectsofproteinstructureand function.Alltoolsdevelopedbyhisresearchgroupareavailablethroughthefirstinternet serverinthefieldofproteinstructureprediction(PredictProtein),aresourcethathasbeen onlineforover25years.Overthelastseveralyears,hisresearchgrouphasbeenshiftingits focustothedevelopmentofmethodsthatpredictandannotatetheeffectofsequence variationandtheirimplicationsforprecisionmedicineandpersonalizedhealth.
FabianSievers,PhD iscurrentlyapostdoctoralresearchfellowinthelaboratoryofDes HigginsatUniversityCollegeDublin,Ireland.Heworksonmultiplesequencealignment algorithmsand,inparticular,onthedevelopmentofClustalOmega.HereceivedhisPhDin mathematicsfromTrinityCollege,Dublinandhasworkedinindustryinthefieldsof algorithmdevelopmentandhigh-performancecomputing.
MichaelF.Sloma,PhD isadatascientistatXometry,Gaithersburg,MD,USA.Hereceivedhis BAdegreeinChemistryfromWellsCollege.HeearnedhisdoctoraldegreeinBiochemistry inthelaboratoryofDavidMathewsattheUniversityofRochester,wherehisresearch focusedoncomputationalmethodstopredictRNAstructurefromsequence.
W.ScottWatkins,MS isaresearcherandlaboratorymanagerintheDepartmentofHuman GeneticsattheUniversityofUtah,SaltLakeCity,UT,USA.Hehasalong-standinginterest inhumanpopulationgeneticsandevolution.Hiscurrentinterestsincludethedevelopment andapplicationofhigh-throughputcomputationalmethodstomobileelementbiology, congenitalheartdisease,andpersonalizedmedicine.
DavidS.Wishart,PhD isaDistinguishedUniversityProfessorintheDepartmentsof BiologicalSciencesandComputingScienceattheUniversityofAlberta,Edmonton,Alberta, Canada.Dr.Wisharthasbeendevelopingbioinformaticsprogramsanddatabasessincethe early1980sandhasmadebioinformaticsanintegralpartofhisresearchprogramfornearly fourdecades.Hisinterestinbioinformaticsledtothedevelopmentofanumberofwidely usedbioinformaticstoolsforstructuralbiology,bacterialgenomics,pharmaceuticalresearch, andmetabolomics.SomeofDr.Wishart’smostwidelyknownbioinformaticscontributions includetheChemicalShiftIndex(CSI)forproteinsecondarystructureidentificationby nuclearmagneticresonancespectroscopy,PHASTforbacterialgenomeannotation,the DrugBankdatabasefordrugresearch,andMetaboAnalystformetabolomicdataanalysis. Overthecourseofhisacademiccareer,Dr.Wisharthaspublishedmorethan400research papers,withmanybeinginthefieldofbioinformatics.Inadditiontohislong-standing interestinbioinformaticsresearch,Dr.Wisharthasbeenapassionateadvocatefor bioinformaticseducationandoutreach.HeisoneofthefoundingmembersoftheCanadian BioinformaticsWorkshops(CBW)–anationalbioinformaticstrainingprogramthathas taughtmorethan3000studentsoverthepasttwodecades.In2002heestablishedCanada’s firstundergraduatebioinformaticsdegreeprogramattheUniversityofAlbertaandhas personallymentorednearly130undergraduateandgraduatestudents,manyofwhomhave goneontoestablishsuccessfulcareersinbioinformatics.
TyraG.Wolfsberg,PhD istheAssociateDirectoroftheBioinformaticsandScientific ProgrammingCoreattheNationalHumanGenomeResearchInstitute(NHGRI),National InstitutesofHealth(NIH),Bethesda,MD,USA.Herresearchprogramfocusesondeveloping methodologiestointegratesequence,annotation,andexperimentallygenerateddatasothat benchbiologistscanquicklyandeasilyobtainresultsfortheirlarge-scaleexperiments.She maintainsalong-standingcommitmenttobioinformaticseducationandoutreach. Shehas authoredachapterongenomicdatabasesforpreviouseditionsofthistextbook,aswellasa chapterontheNCBIMapViewerfor CurrentProtocolsinBioinformatics and Current ProtocolsinHumanGenetics.Sheservesastheco-chairoftheNIHlectureseriesCurrent TopicsinGenomeAnalysis;theselecturesarearchivedonlineandhavebeenviewedover 1milliontimestodate.InadditiontoteachingbioinformaticscoursesatNHGRI,sheserved for13yearsasafacultymemberinbioinformaticsattheannualAACRWorkshopon MolecularBiologyinClinicalOncology.
MichaelZuker,PhD retiredasaProfessorofMathematicalSciencesatRensselaerPolytechnic Institute,Troy,NY,USA,in2016.HewasanAdjunctProfessorintheRNAInstituteatthe UniversityofAlbanyandremains affiliatedwiththeRNAInstitute.Heworksonthe developmentofalgorithmstopredictfolding,hybridization,andmeltingprofilesinnucleic acids.Hisnucleicacidfoldingandhybridizationwebservershavebeenrunningatthe UniversityofAlbanysince2010.Hiseducationalactivitiesincludedevelopingandteaching hisownbioinformaticscourseatRensselaerandparticipatinginbothaChautauquashort courseinbioinformaticsforcollegeteachersandanintensivebioinformaticscourseatthe UniversityofMichigan.HecurrentlyservesontheScientificAdvisoryBoardofExpansion Therapeutics,Inc.attheScrippsResearchInstituteinJupiter,Florida.
