BENJAMIN J. RAPHAEL - Brown Universitycompbio-research.cs.brown.edu/people/BRaphael_CV.pdf · Dr. Benjamin J. Raphael C.V., January 2017. Page 1 of 23 BENJAMIN J. RAPHAEL Professor

Dr. Benjamin J. Raphael C.V., January 2017. Page 1 of 23

BENJAMINJ.RAPHAELProfessor

DepartmentofComputerSciencePrincetonUniversity35OldenStreet

Princeton,NJ08540

Phone:(609)258-6314 Email:[email protected] Web:http://compbio.cs.brown.eduEDUCATION1996-2002 Ph.D.inMathematics,UniversityofCalifornia,SanDiego.

ThesisTitle:AComputationalInvestigationofSpectralSetsandRationalDilationsoverMultiply-ConnectedDomains.Advisor:ProfessorJimAgler.

1992-1996 S.B.inMathematics,S.B.MinorinBiology,MassachusettsInstituteofTechnology.

EXPERIENCE2016- Professor,DepartmentofComputerScience,PrincetonUniversity2016- FounderandConsultant,MedleyGenomics,Providence,RI2013-2016 Director,CenterforComputationalMolecularBiology,BrownUniversity2011-2016 AssociateProfessor,DepartmentofComputerScience&Centerfor

ComputationalMolecularBiology,BrownUniversity2006-2011 AssistantProfessor,DepartmentofComputerScience&Centerfor

ComputationalMolecularBiology,BrownUniversity2005-2006 BurroughsWellcomePostdoctoralFellowshipinComputerScience

(Bioinformatics),UniversityofCalifornia,SanDiego.Sponsor:ProfessorPavelPevzner.

2002-2004 AlfredP.SloanPostdoctoralFellowshipinComputerScience(Bioinformatics),UniversityofCalifornia,SanDiego.Sponsor:ProfessorPavelPevzner.

PUBLICATIONSAuthorordergenerallyfollowsconventioninbiology,withsenior/correspondingauthorlistedlast.Underlinedauthorsaretrainees.†indicatesundergraduates.*indicatesjointfirstorlastauthor.RefereedJournalandConferenceResearchPapersS.Zaccaria*,M.El-Kebir*,G.W.Klau,B.J.Raphael.(2017)TheCopy-NumberTreeMixtureDeconvolutionProblemandApplicationstoMulti-SampleBulkSequencingTumorData.RECOMB2017.


TheCancerGenomeAtlasResearchNetwork.(2017)Integratedgenomiccharacterizationofoesophagealcarcinoma.Nature541(7636):169-175.M.D.M.Leiserson,M.A.Reyna,B.J.Raphael.(2016).AWeightedExactTestforMutuallyExclusiveMutationsinCancer.ECCB2016/Bioinformatics,32(17):i736-i745.P.Nakka,B.J.Raphael*,SRamachandran*(2016)GeneandNetworkAnalysisofCommonVariantsRevealsNovelAssociationsinMultipleComplexDiseases.Genetics,204(2):783-798.M.El-Kebir*,G.Satas*,L.Oesper,B.J.Raphael(2016).InferringtheMutationalHistoryofaTumorusingMulti-StatePerfectPhylogenyMixtures.CellSystems,3(1):43-53.OntheSampleComplexityofCancerPathwaysIdentification.(2016)F.Vandin,B.J.Raphael,E.Upfal.JournalofComputationalBiology23(1):30-41.M.El-Kebir,B.J.Raphael,R.Shamir,R.Sharan,S.Zaccaria,M.Zehavi,R.Zeira.(2016)Copy-NumberEvolutionProblems:ComplexityandAlgorithmsWorkshoponAlgorithmsforBioinformatics(WABI)2016.M.El-Kebir,G.Satas,L.Oesper,B.J.Raphael(2016).Multi-StatePerfectPhylogenyMixtureDeconvolutionandApplicationstoCancerSequencing.RECOMB2016S.Zheng,A.D.Cherniack,N.Dewal,R.A.Moffitt,L.Danilova,B.A.Murray,A.M.Lerario,T.Else,T.A.Knijnenburg,G.Ciriello,S.Kim,G.Assie,O.Morozova,R.Akbani,J.Shih,K.A.Hoadley,T.K.Choueiri,J.Waldmann,O.Mete,A.G.Robertson,B.J.Raphael,M.Meyerson,M.J.Demeure,F.Beuschlein,A.J.Gill,A.C.Latronico,M.C.Fragoso,L.M.Cope,E.Kebebew,M.A.Habra,T.G.Whitsett,K.J.Bussey,W.E.Rainey,S.L.Asa,J.Bertherat,M.Fassnacht,D.A.Wheeler,TheCancerGenomeAtlasResearchNetwork,G.D.Hammer*,T.J.Giordano*,R.G.W.Verhaak*.(2015)ComprehensivePan-GenomicCharacterizationofAdrenocorticalCarcinoma.CancerCell.(2016)29(5):723-36.C.Weinreb†andB.J.Raphael(2016).Identificationofhierarchicalchromatindomains.Bioinformatics.32(11):1601-9.C.Lu*,M.Xie*,M.C.Wendl*,J.Wang*,M.D.McLellan*,M.D.M.Leiserson*,M.A.Wyczalkowski,R.Jayasinghe,K.Huang,T.Banerjee,J.Ning,P.Tripathi,Q.Zhang,B.Niu,K.Ye,H.K.Schmidt,R.S.Fulton,J.F.McMichael,P.Batra,C.Kandoth,M.Bharadwaj,D.C.Koboldt,C.A.Miller,K.L.Kanchi,J.M.Eldred,D.E.Larson,J.S.Welch,M.You,B.A.Ozenberger,R.Govindan,M.J.Walter,M.J.Ellis,E.R.Mardis,T.A.Graubert,J.F.Dipersio,T.J.Ley,R.K.Wilson,P.J.Goodfellow,B.J.Raphael,F.Chen,K.J.Johnson,J.D.Parvin,L.Ding.(2015)PatternsandFunctionalImplicationsofRareGermlineVariantsacross12CancerTypes.NatureCommunications.6:10086.


TheCancerGenomeAtlasResearchNetwork.(2015)ComprehensiveMolecularCharacterizationofPapillaryRenalCellCarcinoma.NewEnglandJournalofMedicine.374(2):135-45.M.D.M.Leiserson,H-T.Wu,F.Vandin,B.J.Raphael(2015).Comet:AStatisticalApproachtoIdentifyCombinationsofMutuallyExclusiveAlterationsinCancer.GenomeBiology16:160.M.D.M.Leiserson,C.C.Gramazio,J.Hu†,H.Wu,D.H.Laidlaw,B.J.Raphael.(2015)MAGI:VisualizationandCollaborativeAnnotationofGenomicAberrations.NatureMethods12(6):483-484.M.El-Kebir*,L.Oesper*,H.Acheson-Field†,B.J.Raphael.(2015)Reconstructionofclonaltreesandtumorcompositionfrommulti-samplecancersequencingdata.Bioinformatics[ProceedingsofISMB2015].31(12):i62-i70.S.M.Doris,D.R.Smith,J.N.Beamesderfer,B.J.Raphael,J.A.Nathanson,S.A.Gerbi.(2015)UniversalandDomain-SpecificSequencesin23S-28SRibosomalRNAIdentifiedbyComputationalPhylogenetics.RNA.(10):1719-30.B.J.Raphael,F.Vandin(2015).SimultaneousInferenceofCancerPathwaysandTumorProgressionfromCross-SectionalMutationData.JournalofComputationalBiology22(6):510-27.M.M.Parks,C.E.Lawrence,B.J.Raphael.(2015)Detectingnon-allelichomologousrecombinationfromhigh-throughputsequencingdata.GenomeBiology16(1),72.F.Vandin,A.Papoutsaki,B.J.Raphael*,E.Upfal*.(2015)AccurateComputationofSurvivalStatisticsinGenome-wideStudies.PLOSComputationalBiology.11(5):e1004071.*correspondingauthorsM.D.M.Leiserson,H-T.Wu,F.Vandin,B.J.Raphael(2015).Comet:AStatisticalApproachtoIdentifyCombinationsofMutuallyExclusiveAlterationsinCancer.19thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2015),202-204.F.Vandin,B.J.Raphael,E.Upfal(2015)OntheSampleComplexityofCancerPathwaysIdentification.19thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2015),326-337.M.D.MLeiserson*,F.Vandin*,H.Wu,J.R.Dobson,J.V.Eldridge,J.L.Thomas†,A.Papoutsaki,Y.Kim†,B.Niu,M.McLellan,M.S.Lawrence,A.Gonzalez-Perez,D.Tamborero,Y.Cheng,G.A.Ryslik,N.Lopez-Bigas,G.Getz,L.Ding,B.JRaphael.(2015)Pan-CancerNetworkAnalysisIdentifiesCombinationsofRareSomaticMutationsacrossPathwaysandProteinComplexes.NatureGenetics.47(2):106-114.


L.Oesper,G.Satas,B.J.Raphael.(2014)QuantifyingTumorHeterogeneityinWhole-GenomeandWhole-ExomeSequencingData.Bioinformatics.30(24):3532-40.A.Ritz,A.Bashir,S.Sindi,D.Hsu,I.Hajirasouliha,B.J.Raphael.(2014).CharacterizationofStructuralVariantswithSingleMoleculeandHybridSequencingApproaches.Bioinformatics.30(24):3458-66.IntegratedGenomicCharacterizationofPapillaryThyroidCarcinoma.(2014)TheCancerGenomicAtlasResearchNetwork.Cell159(3):676-90.C.Weinreb†,L.Oesper,B.J.Raphael.(2014)Openadjacenciesandk-breaks:detectingsimultaneousrearrangementsincancergenomes.BMCGenomics15(Suppl6):S4.Specialissueforthe12thAnnualResearchinComputationalMolecularBiology(RECOMB)SatelliteWorkshoponComparativeGenomics(RECOMB-CG2014)K.A.Hoadley*,C.Yau*,D.M.Wolf*,A.D.Cherniack*,D.Tamborero,S.Ng,M.D.M.Leiserson,B.Niu,M.D.McLellan,E.O.Paull,V.Uzunangelov,C.Kandoth,R.Akbani,H.Shen,TCGANetwork,L.van’tVeer,N.Lopez-Bigas,P.W.Laird,B.J.Raphael,L.Ding,E.A.Collisson,L.A.Byers,G.B.Mills,J.Weinstein,C.VanWaes,Z.Chen,C.Benz#,C.M.Perou#,J.M.Stuart#(2014)Multi-platformintegrationof12cancertypesrevealscell-of-originclasseswithdistinctmolecularsignatures.Cell158(4):929-944.I.Hajirasouliha,B.J.Raphael.(2014)Reconstructingmutationalhistoryinmultiplysampledtumorsusingperfectphylogenymixtures.14thWorkshoponAlgorithmsinBioinformatics(WABI).TheCancerGenomeAtlasResearchNetwork.(2014)Comprehensivemolecularcharacterizationofgastricadenocarcinoma.Nature513:202-209.H.Wu,I.Hajirasouliha,B.J.Raphael.(2014)Detectingindependentandrecurrentcopynumberaberrationsusingintervalgraphs.Bioinformatics30(12),i195-i203.[Specialissueforthe22ndAnnualInternationalConferenceonIntelligentSystemsinMolecularBiology(ISMB2014)]I.Hajirasouliha*,A.Mahmoody*,B.J.Raphael.(2014)Acombinatorialapproachforanalyzingintra-tumorheterogeneityfromhigh-throughputsequencingdata.Bioinformatics30(12),i78-i86.[Specialissueforthe22ndAnnualInternationalConferenceonIntelligentSystemsinMolecularBiology(ISMB2014)]*equalcontribution.A.S.Brodsky,A.Fischer,D.H.Miller,S.Vang,S.Maclaughlan,H.T.Wu,J.Yu,M.Steinhoff,C.Collins,P.J.Smith,B.J.Raphael,L.Brard.(2014)Expressionprofilingofprimaryandmetastaticovariantumorsrevealsdifferencesindicativeofaggressivedisease.PLoSOne.(2014)9(4):e94476.


B.J.Raphael,F.Vandin(2014)SimultaneousInferenceofCancerPathwaysandTumorProgressionfromCross-SectionalMutationData.18thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB).KanchiKL,JohnsonKJ,LuC,McLellanMD,LeisersonMD,WendlMC,ZhangQ,KoboldtDC,XieM,KandothC,McMichaelJF,WyczalkowskiMA,LarsonDE,SchmidtHK,MillerCA,FultonRS,SpellmanPT,MardisER,DruleyTE,GraubertTA,GoodfellowPJ,RaphaelBJ,WilsonRK,DingL.(2014)Integratedanalysisofgermlineandsomaticvariantsinovariancancer.NatureCommunications5:3156.C.Kandoth,M.D.McLellan,F.Vandin,K.Ye,B.Niu,C.Lu,M.Xie,Q.Zhang,J.F.McMichael,M.A.Wyczalkowski,M.D.M.Leiserson,C.A.Miller,J.S.Welch,M.J.Walter,M.C.Wendl,T.J.Ley,R.K.Wilson,B.J.RaphaelL.Ding.(2013)Mutationallandscapeandsignificanceacross12majorcancertypes.Nature502(7471):333-9.[PublisherLink]TheCancerGenomeAtlasResearchNetwork.(2013)TheCancerGenomeAtlasPan-Canceranalysisproject.NatureGenetics45(10):1113-20.[PublisherLink]L.Oesper,A.Mahmoody,B.J.Raphael.(2013)THetA:Inferringintra-tumorheterogeneityfromhigh-throughputDNAsequencingdata.GenomeBiology14:R80.[PublisherLink][SupplementalMaterial]TheCancerGenomeAtlasResearchNetwork.(2013)Comprehensivemolecularcharacterizationofclearcellrenalcellcarcinoma.Nature499(7456):43-9.[PublisherLink]HoAS,KannanK,RoyDM,MorrisLG,GanlyI,KatabiN,RamaswamiD,WalshLA,EngS,HuseJT,ZhangJ,DolgalevI,HubermanK,HeguyA,VialeA,DrobnjakM,LevershaMA,RiceCE,SinghB,IyerNG,LeemansCR,BloemenaE,FerrisRL,SeethalaRR,GrossBE,LiangY,SinhaR,PengL,RaphaelBJ,TurcanS,GongY,SchultzN,KimS,ChioseaS,ShahJP,SanderC,LeeW,ChanTA.(2013)Themutationallandscapeofadenoidcysticcarcinoma.NatureGenetics45(7):791-8.[PublisherLink]M.D.M.Leiserson,D.Bloch,R.Sharan*,B.J.Raphael*.(2013)SimultaneousIdentificationofMultipleDriverPathwaysinCancer.PLOSComputationalBiology.May;9(5):e1003054.[PublisherLink]*equalcontribution.TheCancerGenomeAtlasResearchNetwork.(2013)GenomicandEpigenomicLandscapesofAdultDeNovoAcuteMyeloidLeukemia.NewEnglandJournalofMedicine.368(22):2059-74.[PublisherLink].[Interativevisualization]L.Oesper,A.Mahmoody,B.J.Raphael.(2013)EstimatingTumorPurityandCancerSubpopulationsfromHigh-ThroughputDNASequencingData.17thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2013).[PublisherLink]


F.Vandin,A.Papoutsaki,B.J.Raphael*,E.Upfal*.(2013)Genome-WideSurvivalAnalysisofSomaticMutationsinCancer.17thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2013).[BestPaperAward,RECOMB2013][PublisherLink]*equalcontribution.F.Vandin,E.Upfal,B.J.Raphael.(2012)FindingDriverPathwaysinCancer:ModelsandAlgorithms.AlgorithmsforMolecularBiol.7(1):23.A.Mahmoody,C.L.Kahn,B.J.Raphael.(2012)ReconstructingGenomeMixturesFromPartialAdjacencies.BMCBioinformatics13Suppl19:S9.[ProceedingsoftheTenthAnnualRECOMBSatelliteWorkshoponComparativeGenomics.]C.Grasso,Y.Wu,D.Robinson,X.Cao,S.Dhanasekaran,A.Khan,M.Quist,X.Jing,R.Lonigro,J.C.Brenner,I.Asangani,B.Ateeq,S.Chun,J.Siddiqui,L.Sam,M.Anstett,R.Mehra,J.Prensner,N.Palanisamy,G.Ryslik,F.Vandin,B.J.Raphael,L.Kunju,D.Rhodes,K.Pienta,A.M.Chinnaiyan,S.A.Tomlins.(2012)TheMutationalLandscapeofLethalCastrateResistantProstateCancer.Nature487(7406):239-43.L.Cao,Y.Ding,N.Hung,K.Yu,A.Ritz,B.J.Raphael,A.R.Salomon.(2012)QuantitativePhosphoproteomicsRevealsSLP-76DependentRegulationofPAGandSrcFamilyKinasesinTCells.PLOSOne.7(10):e46725.R.H.Palmer,J.E.McGeary,S.Francazio,B.J.Raphael,A.D.Lander,A.C.Heath,V.S.Knopik.(2012)Thegeneticsofalcoholdependence:Advancingtowardssystems-basedapproaches.DrugAlcoholDepend.125(3):179-91.S.Sindi,S.Onal,L.Peng,H.Wu,B.J.Raphael.(2012)AnIntegrativeProbabilisticModelforIdentificationofStructuralVariationinSequencingData.GenomeBiology13(3):R22.L.Oesper,A.Ritz,S.J.Aerni,R.Drebin†,B.J.Raphael(2012)ReconstructingCancerGenomeOrganization.BMCBioinformatics(Proceedingsof2ndRECOMBSatelliteWorkshoponMassivelyParallelSequencing(RECOMB-seq)).13(Suppl6):S10A.Caceres,S.SSindi,B.JRaphael,M.CaceresandJ.RGonzalez.(2012)IdentificationofPolymorphicInversionsfromGenotypes.BMCBioinformatics13(1):28F.Vandin,P.Clay†,E.Upfal,B.J.Raphael.(2012)DiscoveryofMutatedSubnetworksAssociatedwithClinicalDatainCancer.PacificSymposiumonBiocomputing.55-66.TheCancerGenomeAtlasResearchNetwork.(2011)IntegratedGenomicAnalysesofOvarianCarcinoma.Nature.474(7353):609-15.F.Vandin,E.Upfal,B.J.Raphael.(2011)DenovoDiscoveryofMutatedDriverPathwaysinCancer.GenomeResearch.22(2):375-85.[JournalversionofpaperacceptedatProceedingsofthe15thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2011)].


A.Stuckey,A.Fischer,D.HMiller,S.Hillenmeyer,K.KKim,A.Ritz,R.KSingh,B.J.Raphael,L.BrardandA.S.Brodsky.(2011)IntegratedGenomicsofOvarianXenograftTumorProgressionandChemotherapyResponse.BMCCancer.Jul22;11:308K.H.Lim,L.Ferraris,M.Filloux,B.J.Raphael,W.Fairbrother.(2011)UsingpositionaldistributiontoidentifysplicingelementsandpredictmRNAprocessingdefectsinhumangenes.ProceedingsoftheNationalAcademyofSciences(PNAS). 108(27):11093-8.F.Vandin,E.Upfal,B.J.Raphael.(2011)FindingDriverPathwaysinCancer:ModelsandAlgorithms.ProceedingsoftheWorkshoponAlgorithmsinBioinformatics(WABI).LectureNotesinComputerScience,Vol.6833.314-315.A.Ritz,P.L.Paris,M.M.Ittmann,C.Collins,andB.J.Raphael.(2011)DetectionofRecurrentRearrangementBreakpointsfromCopyNumberData.BMCBioinformatics.12:114.VandinF,UpfalE,B.J.Raphael.(2011)AlgorithmsforDetectingSignificantlyMutatedPathwaysinCancer.JournalofComputationalBiology.18(3):507-22.T.O'Brien,A.Ritz,B.J.Raphael,andD.H.Laidlaw.(2010)Gremlin:AnInteractiveVisualizationModelforAnalyzingGenomicRearrangements.IEEETrans.onVisualizationandComputerGraphics(Proc.IEEEInformationVisualizationConference2010)16(6):918-26.C.L.Kahn,B.H.Hristov†,andB.J.Raphael.(2010)ParsimonyandLikelihoodReconstructionofHumanSegmentalDuplications.Bioinformatics(Proceedingsofthe9thEuropeanConferenceonComputationalBiology).26(18):i446-52.InternationalCancerGenomeConsortium.(2010)Internationalnetworkofcancergenomeprojects.Nature.464(7291):993-8.A.Ritz,A.Bashir,andB.J.Raphael.(2010)StructuralVariationAnalysiswithStrobeReads.Bioinformatics.26(10):1291-8.F.Vandin,E.Upfal,andB.J.Raphael.(2010)AlgorithmsforDetectingSignificantlyMutatedPathwaysinCancer.Proceedingsofthe14thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2010).LectureNotesinComputerScience,Volume6044,506-521.C.L.Kahn,S.Mozes,andB.J.Raphael.(2010)EfficientAlgorithmsforAnalyzingSegmentalDuplicationswithDeletionsandInversionsinGenomes.AlgorithmsforMolecularBiology.5(1):11.S.SindiandB.J.Raphael.(2010)IdentificationandFrequencyEstimationofInversionPolymorphismsfromHaplotypeData.JournalofComputationalBiology.17(3):517-31.


A.Bashir,Q.Liu,B.J.Raphael,D.Carson,Y.T.Liu,V.Bafna.OptimizingPCRassaysforDNAbasedcancerdiagnostics.(2010)JournalofComputationalBiology.17(3):369-81.C.L.Kahn,S.Mozes,andB.J.Raphael.(2009)EfficientAlgorithmsforAnalyzingSegmentalDuplications,Deletions,andInversionsinGenomes.WorkshoponAlgorithmsinBioinformatics(WABI).169-180.V.Nguyen,L.Cao,J.T.Lin,N.Hung,A.Ritz,K.Yu,R.Jianu,S.P.Ulin,B.J.Raphael,D.H.Laidlaw,L.Brossay,A.R.Salomon.(2009)ANewApproachforQuantitativePhosphoproteomicDissectionofSignalingPathwaysAppliedtoTcellReceptorActivation.MolecularandCellularProteomics.8(11):2418-31.S.Sindi,E.Helman†,A.Bashir,B.J.Raphael.(2009)AGeometricApproachforClassificationandComparisonofStructuralVariants.Bioinformatics25:i222-i230.[ProceedingsoftheJoint17thAnnualInternationalConferenceonIntelligentSystemsinMolecularBiologyand8thAnnualInternationalEuropeanConferenceonComputationalBiology(ISMB/ECCB09)]S.SindiandB.J.Raphael.IdentificationandFrequencyEstimationofInversionPolymorphismsfromHaplotypeData.(2009)Proceedingsofthe13thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2009).A.Bashir,Q.Liu,B.J.Raphael,D.Carson,Y.T.Liu,V.Bafna.OptimizingPCRassaysforDNAbasedcancerdiagnostics.(2009)Proceedingsofthe13thAnnualInternationalConferenceonResearchinComputationalMolecularBiology(RECOMB2009).C.L.KahnandB.J.Raphael.AParsimonyApproachtoAnalysisofHumanSegmentalDuplications.(2009)PacificSymposiumonBiocomputing.14:126-137.B.T.Messmer*,B.J.Raphael*,S.J.Aerni†,G.FWidhopf,L.ZRassenti,T.LToy,T.JKipps.(2009)ComputationalIdentificationAndClinicalRelevanceOfCDR3SequenceArchetypesAmongCLLIGHVSequences.LeukemiaResearch.33(3):368-76.*equalcontributionA.Ritz,G.Shakhnarovich,A.R.Salomon,B.J.Raphael.(2009)IdentificationofPhosphorylationMotifMixturesinPhosphoproteomicsData.Bioinformatics.25(1):14-21.C.L.KahnandB.J.Raphael.AnalysisofSegmentalDuplicationsviaDuplicationDistance.(2008)Bioinformatics.24(16):i133-8(ProceedingsoftheEuropeanConferenceonComputationalBiology).B.J.Raphael,S.Volik,G.Huang,F.Waldman,J.Costello,S.Aerni†,R.P.Brown†,A.Bashir,K.Pienta,G.Mills,K.Bajsarowicz,P.Paris,Q.Tao,W.Kuo,J.W.Gray,J.Cheng,M.Nefedov,P.deJong,andC.Collins.(2008).Asequencebasedsurveyofthecomplexstructuralorganizationoftumorgenomes.GenomeBiology.9(3):R59.[Designated“HighlyAccessed]


A.Bashir,S.Volik,C.C.Collins,V.Bafna,B.J.Raphael.(2008)EvaluationofPaired-endSequencingStrategiesforDetectionofGenomeRearrangementsinCancer.PLOSComputationalBiology.4(4):e1000051.J.Agler,J.Harland,B.J.Raphael.(2008)ClassicalFunctionTheory,OperatorDilationTheory,andMachineComputationonMultiply-ConnectedDomains.MemoirsoftheAmericanMathematicalSociety.Vol.191,No.892.A.Bashir,Y.T.Liu,B.J.Raphael,D.Carson,V.Bafna.(2007)Optimizationofprimerdesignforthedetectionofvariablegenomiclesionsincancer.Bioinformatics.23(21):2807-15.L.Cao,K.Yu,V.Nguyen,A.Ritz,B.J.Raphael,Y.Kawakami,T.Kawakami,A.R.Salomon,(2007)QuantitativeTime-ResolvedPhosphoproteomicAnalysisofMastCellSignaling.JournalofImmunology.179(9):5864-76.E.Corona,B.J.Raphael,E.Eskin.(2007)IdentifyingDeletionPolymorphismsfromHaplotypes.Proceedingsofthe11ThAnnualInternationalConferenceonResearchinComputationalBiology(RECOMB2007).pg.354-365.S.Yooseph,G.Sutton,D.B.Rusch,A.L.Halpern,S.J.Williamson,K.Remington,J.A.Eisen,K..B.Heidelberg,G.Manning,W.Li,L.Jaroszewski,P.Cieplak,C.S.Miller,H.Li,S.T.Mashiyama,M.P.Joachimiak,C.vanBelle,J.Chandonia,D.A.Soergel,Y.Zhai,K.Natarajan,S.Lee,B.J.Raphael,V.Bafna,R.Friedman,S.E.Brenner,A.Godzik,D.Eisenberg,J.E.Dixon,S.S.Taylor,R.L.Strausberg,M.Frazier,J.C.Venter.(2007)TheSorcererIIGlobalOceanSamplingExpedition:ExpandingtheUniverseofProteinFamilies.PLOSBiology.5(3):e16.M.Chaisson,B.J.Raphael,andP.Pevzner.(2006)Micro-inversionsinMammalianEvolution.ProceedingsoftheNationalAcademyofSciences,USA.103(52):19824-9.N.C.Jones,D.Zhi,B.J.Raphael.(2006)AliWABA:AlignmentontheWebthroughanA-BruijnApproach.NucleicAcidsResearch.July1;34:W613-6.S.Volik,B.J.Raphael,Huang,G.,Stratton,M.R.,Bignel,G.,Murnane,J.,Brebner,J.H.,Bajsarowicz,K.,Paris,P.L.,Tao,Q.,Kowbel,D.,Lapuk,A.,Shagin,D.A.,Shagina,I.A.,Gray,J.W.,Cheng,J.,deJong,P.J.,Pevzner,P.,andCollins,C.(2006)DecodingtheFine-scaleArchitectureofaBreastCancerGenomeandTranscriptome.GenomeResearch,16(3):394-404.D.Zhi,B.J.Raphael,A.Price,H.Tang,P.Pevzner.(2006)IdentifyingRepeatDomainsinLargeGenomes.GenomeBiology,7(1):R7.[Designated“HighlyAccessed”]B.J.Raphael,D.Zhi,H.Tang,P.Pevzner.(2004)ANovelMethodforMultipleAlignmentofSequenceswithRepeatedandShuffledDomains.GenomeResearch,14(11):2336-46.B.J.RaphaelandP.Pevzner.(2004)ReconstructingTumorAmplisomes.Bioinformatics,20Suppl1:I265-I273.(SpecialISMB/ECCB2004Issue).[Selectedby“Facultyof1000”]


B.J.Raphael,L.Liu,andG.Varghese.(2004)AUniformProjectionMethodforMotifDiscoveryinDNASequences.IEEETransactionsonComputationalBiologyandBioinformatics,1(2):91-94.B.J.Raphael,S.Volik,C.Collins,P.Pevzner.(2003)ReconstructingTumorGenomeArchitectures.Bioinformatics,Suppl2:ii162-171.(SpecialECCB2003Issue).[Selectedby“Facultyof1000”]BooksandEditedVolumesB.J.Raphael,J.Tang(Eds.).(2012)AlgorithmsinBioinformatics-12thInternationalWorkshop,WABI2012,Ljubljana,Slovenia,September10-12,2012.Proceedings.LectureNotesinComputerScience7534,Springer.E.Eskin,T.Ideker,B.J.Raphael,C.Workman(eds.),(2006)SystemsBiologyandRegulatoryGenomics.JointAnnualRECOMB2005SatelliteWorkshopsonSystemsBiologyandonRegulatoryGenomics.LectureNotesinComputerScience,Vol.4023.Springer-Verlag.BookChaptersandReviewArticlesP.Creixell,J.Reimand,S.Haider,G.Wu,T.Shibata,M.Vazquez,V.Mustonen,A.Gonzalez-Perez,J.Pearson,C.Sander,B.J.Raphael,D.S.Marks,B.F.F.Ouellette,A.Valencia,G.D.Bader,P.C.Boutros,J.M.Stuart,R.Linding,N.Lopez-Bigas,L.D.Stein,MutationConsequencesandPathwayAnalysisWorkingGroupoftheInternationalCancerGenomeConsortium.(2015)PathwayandNetworkAnalysisofCancerGenomes.NatureMethods.12(7):615-621.S.Brunak,F.M.DeLaVega,A.Margolin,B.J.Raphael,G.Raetsch,J.M.Stuart.(2015)CancerPanomics:ComputationalMethodsandInfrastructureforIntegrativeAnalysisofCancerHigh-Throughput“Omics”Data.PacificSymposiumonBiocomputing(PSB)2015.20:8-9.M.D.M.LeisersonandB.J.Raphael.(2015)AnalyzingCombinationsofSomaticMutationsinCancerGenomes.In:Integrating-omicsdata:StatisticalandComputationalMethods.G.C.Tseng,D.Ghosh,X.J.Zhou,(Eds.)CambridgeUniversityPress.L.DingL,M.C.Wendl,J.F.McMichael,B.J.Raphael.(2014)Expandingthecomputationaltoolboxforminingcancergenomes.NatureReviewsGenetics.(8):556-70.B.J.Raphael,J.R.Dobson,L.Oesper,andF.Vandin(2014)Identifyingdrivermutationsinsequencedcancergenomes:computationalapproachestoenableprecisionmedicine.GenomeMedicine.6:5.S.S.Sindi,B.J.Raphael(2014).IdentificationofStructuralVariation.InGenomeAnalysis:CurrentProcedures.M.S.Poptsova(ed).CaisterAcademicPress.


M.D.M.Leiserson,J.V.Eldridge,S.Ramachandran,B.J.Raphael.NetworkAnalysisofGWASData.CurrentOpinioninGenetics&Development(2013)23(6):602-10.[PublisherLink]B.J.Raphael(2013).Makingconnections:usingnetworkstostratifyhumantumors(NewsandViews).NatureMethods10(11):1077-8.[PublisherLink]L.Ding,B.J.Raphael,F.Chen,M.C.Wendl.(2013)AdvancesforStudyingClonalEvolutioninCancer.CancerLetters.pii:S0304-3835(13)00034-7.[PublisherLink]E.Batchelor,M.G.Kann,T.M.Przytycka,B.J.Raphael,D.Wojtowicz.(2013)Modelingcellheterogeneity:fromsingle-cellvariationstomixedcells.PacificSymposiumonBiocomputing(PSB)2013.18:445-50.[PublisherLink]G.Bebek,M.Koyutürk,T.Laframboise,B.J.Raphael,M.R.Chance(2013).Post-NGS:InterpretationandAnalysisofNextGenerationSequencingDataforBasicandTranslationalScience.PacificSymposiumonBiocomputing(PSB)2013.18:307-309.B.J.Raphael.(2012)StructuralVariationandMedicalGenomics.PLOSComputationalBiology.8(12):e1002821.F.Vandin,E.Upfal,B.J.Raphael.(2012)AlgorithmsandGenomeSequencing:IdentifyingDriverPathwaysinCancer.IEEEComputerMarch2012(vol.45no.3)pp.39-46.B.J.Raphael,S.Volik,C.Collins(2007).AnalysisofGenomicAlterationsinCancer.InGenomeSequencingTechnologyandAlgorithms.H.Tang,S.Kim,E.Mardis(eds).ArtechHousePublishers.WorkinReviewPatentsB.J.Raphael,M.D.M.Leiserson,F.Vandin,H.Wu(2015).HeatDiffusionBasedGeneticNetworkAnalysis.U.S.PatentApplicationNo.:62/057,479.B.J.Raphael,M.El-Kebir.G.Satas.(2016).PhylogenyTreeGenerationFromMixedSamples.U.S.ProvisionalPatentApplicationNo.:62/440,563.InvitedTalks2016 SimonsInstitutefortheTheoryofComputing,GenomicsBootcamp

SimonsInstitutefortheTheoryofComputing,NetworksBiologyWorkshopMichaelWaterman75thBirthdaySymposiumSystemsApproachestoCancerBiologyConference.WeillCornell,InstituteforComputationalBiomedicine(ICB)SeminarUniversityofPennsylvania,PennBioinformaticsForum


InternationalSymposiumonPancreaticCancer 5thSeoulNationalUniversityBioinformaticsWorkshop UCLAComputationalGenomicsSummerInstitute 1stAnnualCancerCellMapInitiativeSymposium SimonsFoundation,NewYork.InvitedLecture

MicrosoftResearchNewEngland.ComputationalAspectsofBiologicalInformation(CABI)Conference

UniversityofToronto,MolecularGeneticsSeminar.2015 Princeton,DepartmentofComputerScience,Seminar RhodeIslandHospital,DepartmentofPathologySeminar McGillBarbadosComputationalBiologyWorkshop

ETH,Zurich:DepartmentofBiosystemsScienceandEngineeringNovartis,Basel,SwitzerlandAstraZenca,Waltham,MAMIT,MathematicsandCSAILBioinformaticsSeminarPompeuFabraUniversity,Barcelona.COSTActionforPancreasCancerWorkshop,Barcelona.FoundationMedicine,Cambridge,MA.TheCancerGenomeAtlas(TCGA),SteeringCommitteeMeeting.StanfordUniversity,CancerSystemsBiologySymposiumCarnegieMellonUniversity,ComputationalBiologySeminarEuropeanLaboratoryforMolecularBiology(EMBL),CancerGeneticsMeetingRECOMBWorkshoponBioinformaticsEducation(RECOMB-BE)CAS-MPGPartnerInstituteforComputationalBiology,ShanghaiCSHA/AACRJointMeeting:BigData,ComputationandSystemsBiologyinCancerIndianaUniversity,DepartmentofComputerScienceSeminarJacksonLaboratoryforGenomicMedicine,Seminar

2014 VanderbiltUniversity:DepartmentofSeminar

U.IllinoisUrbanaChampaign:InstituteforGenomicBiologySeminarCambridgeHealthtech:MolecularMedicineTri-ConferenceKeynote:RECOMBWorkshoponMassivelyParallelSequencing.InvitedTalk:AmericanAssociationofCancerResearch(AACR)AnnualMeetingTuftsUniversity:DepartmentofComputerScienceSeminarSeminar:Novartis,CambridgeInvitedTalk:InstituteforPureandAppliedMathematics(IPAM)InvitedTalk:GEResearchKeynote:VarI-SIGatIntelligentSystemsforMolecularBiology(ISMB)conferenceBioConductorAnnualMeetingEuropeanConferenceonComputationalBiology(ECCB)WorkshopKavliInstituteforTheoreticalPhysics:EvolutionofDrugResistanceProgramBrownUniversityMPPBDepartmentBeyondtheGenomeConferenceUNCCharlotte:DepartmentofBioinformaticsSeminarBroadInstitute


EMBL:CausalInferenceWorkshopKeynote:UWDepartmentofGenomeSciencesSymposiumBostonUniversity:SystemsBiologySeminar

2013 ColdSpringHarborSystemsBiology:NetworksMeeting AmericanAssociationofCancerResearch(AACR)AnnualMeeting

TCGAPan-CancerSymposiumIlluminaSequencingExpertPanel

InstituteforPureandAppliedMathematics,UCLA,ProgramReunion BertinoroComputationalBiologyConference RhodeIslandCollegeBiologySymposium Genentech

InternationalCancerGenomeConsortium(ICGC)AnnualMeeting AmericanSocietyHumanGenetics(ASHG)AnnualMeeting MicrosoftResearch,NewEngland2012 InternationalCancerGenomeConsortium(ICGC)AnnualMeeting

ColdSpringHarborQuantitativeBiologySeminarTheCancerGenomeAtlas(TCGA)SecondScientificSymposiumVancouverBioinformaticsGroup(VanBUG)TCGAPan-CancerWorkshopBeyondtheGenomeConference,Boston,MAJointStatisticalMeetingsSessionon“DesignandAnalysisIssueswithNext-

GenerationSequencingDataonComplexTraits”,San,Diego,CA.PacificSymposiumonBiocomputing,GenomicMedicineSession.

CanadianInstituteforAdvancedResearch,GeneticNetworksMeeting.2011 ProgramFinalRetreat,InstituteforPureandAppliedMathematics,UCLA

BioinformaticsRendezvous,GenomeQuebec,Montreal,CanadaTheCancerGenomeAtlas'1stAnnualScientificSymposiumCancerGenomicsWorkshop,InstituteforPureandAppliedMathematics,UCLAWorkshop,StatisticalAnalysisforNextGenerationSequencing,Birmingham,ALKnightCancerCenter,OregonHealthSciencesUniversity,SeminarThirdRECOMBSatelliteConferenceonBioinformaticsEducationAscona,SwizerlandWorkshop:“StatisticalChallengesandBiomedicalApplicationsofDeepSequencingData”.CambridgeHealthtechInstitute,“X-GenCongressandExposition”UniversityofCalifornia,SanDiego.BioinformaticsSeminar.

UniversityofCalifornia,LosAngeles.ComputerScienceSeminar.IEEEWorkshoponComputationalAdvancesforNextGenerationSequencing(CANGS2011).UniversityofChicago,DepartmentsofStatisticsandCancerBiologySeminar.

2010 MathematicalAssociationofAmerica,NortheastSectionRegionalMeeting.

WashingtonUniversityinSt.Louis,ComputerScienceSeminar.UniversityofVirginia,BiochemistryandMolecularGeneticsSeminar.


MemorialSloan-KetteringCancerCenter,ComputationalBiologySeminar.NextGenerationSequencingDataAnalysisSymposium,BrownUniversityWashingtonUniversityinSt.Louis,GeneticsSeminar.ColdSpringHarborLaboratory,“PersonalGenomes”MeetingMassachusettsInstituteofTechnology,BioinformaticsSeminar.UniversityofRhodeIslandGenomeInformaticsAlliance(Illumina)SIAMConferenceonDiscreteMathematics

2009 UniversityofCalifornia,Berkeley,MathematicsColloquiumRhodeIslandResearchAllianceSymposium.CambridgeHealthtechInstitute,“Next-GenerationSequenceDataAnalysis”MeetingColdSpringHarborLaboratory,“BiologyofGenomes”MeetingHelicosBioSciences,Cambridge,MA

2008 WashingtonUniversitySt.LouisGenomeSequencingCenterSIAMConferenceonDiscreteMathematicsUniversityofConnecticut,DepartmentofComputerScienceColloquiumUniversityofCalifornia,LosAngeles,BioinformaticsSeminarSecondAnnualBertinoroSystemsBiologyMeeting

2007 MathematicalSciencesResearchInstitute,“MathematicalSystemsBiologyofCancer

II”HarvardMedicalSchool-PartnersHealthcareCenterforGeneticsandGenomicsGEM4ConferenceonCancer,SingaporeFifthAnnualBertinoroComputationalBiologyMeetingUniversityofVirginia,DepartmentofMathematics

SixthAnnualMcGillWorkshoponBioinformaticsinBarbados2006 TuftsUniversity,DepartmentofComputerScience BrownUniversity,CenterforStatisticalSciences

MathematicalSciencesResearchInstitute,“MathematicalSystemsBiologyofCancer”UniversityofCalifornia,SanDiego,DepartmentofMathematicsUniversityofSouthernCalifornia,DepartmentofComputationalandMolecularBiologyUniversityofMinnesota,DepartmentofComputerScienceWashingtonUniversitySt.Louis,DepartmentofGeneticsBostonUniversity,BioinformaticsProgramBrownUniversity,DepartmentofComputerScienceUniversityofCalifornia,Irvine,DepartmentofComputerScienceUniversityofCalifornia,SantaCruz,DepartmentofBimolecularEngineeringFredHutchinsonCancerResearchCenterPurdueUniversity,DepartmentofComputerScienceUniversityofWisconsin,DepartmentofBiomedicalInformaticsMemorialSloan-KetteringCancerCenter


UniversityofMaryland,DepartmentofComputerScienceGeorgiaTech,DepartmentofComputerScienceUniversityofCalifornia,SanDiego,CancerCenter

2004 RECOMBSatelliteMeetingonComparativeGenomics,Bertinoro,ItalyDukeUniversity,DepartmentofComputerScienceNorthCarolinaStateUniversity,BioinformaticsSeminarIntelligentSystemsinMolecularBiology(ISMB),Glasgow,Scotland.

2003 EuropeanConferenceonComputationalBiology(ECCB),Paris,France.RESEARCHGRANTSCurrentNationalCancerInstitute(NCI)U24-CA211000 9/15/2016-8/31/2021PathwayandNetworkIntegrationofCancerGenomicsandClinicalDataRole:PITotalAmount:$1,680,000NationalCancerInstitute(NCI) 9/15/2016-8/31/2021DeepDiscoveryandClinicalInterpretationoftheGermlineandSomaticCancerDriversRole:Co-investigator.PI:L.Ding(UniversityofWashington,St.Louis)TotalAmountofSubaward:$50,000NationalScienceFoundation 1/1/2011-12/31/2017CAREER:AlgorithmsforNext-GenerationGenomicsRole:PITotalAmount:$450,000NIH/NHGRI1R01HG005690 1/01/2011-12/31/2016ComputationalApproachesforStructuralVariationStudiesinGenomesRole:PITotalAmount:$2,616,370NIH/NHGRI1R01HG007069 9/1/2013-8/31/2017ComputationalCharacterizationofGeneticHeterogeneityRole:PITotalAmount:$1,119,000NationalInstitutesofHealthR01GM118652-01 6/1/2016-5/31/2021 NovelstatisticalmethodstolocalizegenomicelementsunderlyingadaptiveevolutionRole:Co-investigator(PI:Ramachandran)NIH 9/1/2015-8/31/2018


MappingOriginsofDNAReplicationintheGenome Role:Co-Investigator(PI:Gerbi)DirectCoststosubaward:~$100KSloanResearchFellowship 9/1/2010-8/31/2016Role:PI TotalAmount:$50,000BurroughsWellcomeCareerAwardattheScientificInterface 1/1/2005-2/15/2017High-resolutionanalysisofTumorGenomeArchitecturesRole:PITotalAmount:$500,000PendingNationalCancerInstitute1U24CA209858A01 7/1/2016–6/30/2021Cloud-enabledIntegrationPlatformforProteogenomicDiscoveryinCancerRole:PI(MPIwithDingandFenyo)CompletedNIH/NationalInstituteofGeneralMedicalSciences 12/1/2014–11/30/2019 COBRECenterforComputationalBiologyofHumanDisease Role:PIofBiomedicalBigDataCore(PI:DavidRand)TotalAmount:$3,556,896[PIoftheBiomedicalBigDataCore.ReliquishedthisroleonmovetoPrinceton.] NationalScienceFoundation 10/1/2012-9/30/2016BIGDATA:Mid-Scale:DA:AnalyticalApproachestoMassiveDataComputationwith

ApplicationstoGenomicsRole:Co-PI(withPI:EliUpfal)TotalAmount:$1,566,685NIH/NCI1R01CA180776-01 6/18/2013-3/31/2017Role:PI(MPI:withEliUpfal)AdditionalfundingfortheNSFBIGDATAawardlistedabove.TotalAmount:$285,316NationalScienceFoundation 8/15/2010-07/31/2015III:Small:AlgorithmicApproachesforPathwayandGeneGroupAnalysisinGeneticStudiesRole:PITotalAmount:$500,000NIH/NIAIDR01AI083636-01A1 6/15/10-5/31/15PhosphoproteomicAnalysisofTCellActivationPathwaysRole:Co-Investigator(PI:ArtSalomon,MCBDepartment,BrownUniversity)


TotalAmount:$1,936,800NationalInstitutesofHealth 7/1/2012-6/30/2015Genome-wideevaluationoftherapeutictargetsforaxonopathiesRole:Co-Investigator(PI:A.DiAntonio,WashingtonUniversityinSt.Louis)TotalAmountofSubcontract:$480,743DODBreastCancerResearchProgramIdeaExpansionAward 9/30/10-9/29/12OriginsofDNAReplicationandAmplificationintheBreastCancerGenomeRole:co-PI(PI:SusanGerbi,MCBDepartment,BrownUniversity)TotalAmount:$607,500.COBRECenterforCancerSignalingNetworksPilotAward 4/01/2012-3/31/2013ComputationalandFunctionalGenomicAnalysisoftheNotchSignalingPathwayinOvarianCancerRole:MPIwithRichardFreiman,BrownMCBTotalAmount:$25,000COBRECenterforCancerSignalingNetworksPilotAward 9/15/2011-9/30/2012MitochondrialGenomicsofCancerRole:Co-PI(PI:DavidRand,BrownMCB)TotalAmount:$52,500Brown-MBLPartnershipSeedFund 9/15/2011-9/30/2012ConservednucleotideelementsinribosomalRNA—targetsignaturesforpathogenicorganismsRole:Co-PI(PI:SusanGerbi,BrownMCB)TotalAmount:$50,000SusanG.KomenFoundation 2008-2011 RoleofEstrogeninBreastCancerGeneAmplificationRole:Co-PI(PI:SusanGerbi) TotalAmount:$480,000DepartmentofDefenseBreastCancerResearchProgram 2007-2009 HormonalInvolvementinBreastCancerAmplificationRole:Co-PI(PI:SusanGerbi,MCBDepartment,BrownUniversity)TotalAmount:$500,000BrownUniversity/Women&InfantsHospitalNationalCenterofExcellenceInWomen’sHealth(CoE)ResearchSeedGrantExploringCisplatinSensitivityofPrimaryandMetastaticOvarianTumorsRole:Co-PI(PI:AlexBrodsky)TotalDirectCosts:$20,000AlfredP.SloanFoundation/DOEFellowshipinComputationalBiology 2002-2004


Role:PITotalAmount:$120,000EDUCATIONGRANTSNationalScienceFoundation,ResearchExperiencesforUndergraduates(REU)SupplementalFundingforSummerUndergraduateResearch.2013:$24,000(Fourstudents)2012:$15,627(Twostudents)SERVICEPrincetonUniversityAdmissionsCommittee,DepartmentofComputerScience2016-2017BrownUniversityDirector,CenterforComputationalMolecularBiology,2013-Member,BiomedicalInformaticsFacultySearchCommittee,2015.Member,BioinformaticsFacultySearchCommittee,2014.Member,PediatricsDepartmentChairSearchCommittee,2013-2014.DirectorofGraduateStudies,ComputationalBiologyPh.D.Program,2011-2013.Member,ComputerScienceDepartmentVisionCommittee,2011-13.Member,FacultyExecutiveCommittee,2010-2011.ExecutiveCommittee,CenterforComputationalMolecularBiology,2006-present.Member,FacultySearchCommittee,CenterforComputationalMolecularBiology,2006-09.Member,GraduateStudentAdmissionsCommittee,Dept.ofComputerScience,2006-12.Member,ResearchComputingandSupportWorkingGroup,2008.SheridanCenterLiaison,ComputerScienceDepartment,2008-2009.LibraryLiaison,ComputerScienceDepartment,2008-2009.Member,StrategicPlanningCommitteeonCenters,Programs&Institutes,2009-10.TotheProfessionSteeringCommittees: RECOMBSatelliteWorkshoponComputationalCancerBiology,2007-present. RECOMBSatelliteWorkshoponMassivelyParallelSequencing,2012-preesnt.ProgramCommittees: ResearchinComputationalMolecularBiology(RECOMB),2011-2017.

IntelligentSystemsinMolecularBiology(ISMB):2010-2016.PacificSymposiumonBiocomputing,2013-2015.RECOMBSatelliteWorkshoponMassivelyParallelSequencing,2014-2015.WorkshoponAlgorithmsinBioinformatics(WABI):2008,2009,2012(Chair),2013,2015.IEEEInternationalConferenceonComputationalAdvancesinBioandMedicalSciences(ICCABS):2011,2012.


ACMConferenceonBioinformatics,ComputationalBiologyandBiomedicine:2011.EuropeanConferenceonComputationalBiology(ECCB):2010,2012.High-ThroughputSequencing(HiTSeq)SiGofISMB,2014,2015FirstInternationalConferenceonBioinformaticsandComputationalBiology(BICoB)2009.InternationalSymposiumonBioinformaticsResearchandApplications,2008.RECOMBSatelliteWorkshoponComputationalCancerBiology.2007(Chair),2010,2015(Co-chair).SixthIEEEInternationalWorkshoponHighPerformanceComputationalBiology(HiCOMB)2007.VLDBWorkshoponDataMininginBioinformatics,2007.

9thAnnualConferenceonComputationalGenomics,2006. RECOMBSatelliteWorkshoponSystemsBiology,2005-2007.

RECOMBSatelliteWorkshoponandRegulatoryGenomics,2005. RECOMBSatelliteWorkshoponComparativeGenomics,2005-2006.OrganizingCommittees: UCLAComputationalGenomicsSummerInstitute,2016-present.

SimonsInstitutefortheTheoryofComputing,ComputationalCancerBiology,2016.MathematicalBiosciencesInstitute,ModelsforOncogenesis,ClonalityandTumorProgression,2016.KeystoneSymposia,TheCancerGenome,2016.InstituteforPureandAppliedMathematics,CancerGenomicsWorkshop,2011.BertinoroComputationalBiology,2008.

RECOMBSatelliteWorkshoponComputationalCancerBiology,2007,2010,2015. SixthAnnualMcGillWorkshoponBioinformaticsinBarbados,2007. RECOMBSatelliteWorkshopsonSystemsBiologyandRegulatoryGenomics, 2005.

RECOMBSatelliteWorkshoponRegulatoryGenomics,2004.JournalReviewing:

Nature,Science,NatureGenetics,NatureBiotechnology,NatureMethods,CellStemCell,ProceedingsoftheNationalAcademyofSciences,GenomeResearch,Bioinformatics,JournalofComputationalBiology(alsoguesteditor),JournaloftheAssociationforComputingMachinery(ACM),ACMTransactionsonAlgorithms,GenomeBiology,TrendsinGenetics,BMCBioinformatics,BMCGenetics,PLOSOne,ParallelComputing.

GrantReviewPanels:

NationalCancerInstituteofCanada,2008,2013.NIHStudySectionMember(adhoc).MABS(2016),BDMA(2012,2013),GCAT

(2012).NationalScienceFoundation,2012NationalHumanGenomeResearchInstitute,2012.NationalCancerInstitute,2011.NationalScienceFoundation,2008,2010,2012.MinistryofEducation,Singapore,2009-2010.


NationalInstituteofGeneralMedicalScience,2008.ScientificAdvisoryCommittees:

NSF-EPSCoRRhodeIslandGenomicsandSequencingCenter,2008-present.Other:

Co-leader,TCGAPancreaticCancerAnalysisWorkingGroup,2014-present.Co-leader,ICGCPan-CancerAnalysisWorkingGrouponNetworks,2014-present.Leader,StructuralAberrationDetectionsubgroup,InternationalCancerGenomeConsortium(ICGC),2010-2013.MemberNIHCancerGenomeAtlas,DataAnalysisGroup,2008-present.CareerPanelMember,HowardHughesMedicalInstituteInterfacesScholarsMeeting,2008.Founder/Member,BioinformaticsConsultingGroup,UCSDComputerScienceDepartment,2004-2006.Founder/Member,GraduateMathematicsConsultingGroup,UCSDMathematicsDepartment,1999-2002.

ProfessionalMemberships:

InternationalSocietyforComputationalBiology,2002-present.AssociationforComputingMachinery,2016-presentAmericanAssociationofCancerResearch,2013-present.AmericanStatisticalSociety,2012-2014.AmericanMathematicalSociety,1996-2002.

HONORS/AWARDSBestPaperAward,RECOMBConference,2013.NationalScienceFoundationCAREERAward,2011.SloanResearchFellowship($50,000),2010.BrownCenterforComputationalMolecularBiology,ResearchSeedAward($5000),2009.BrownADVANCEProgramFacultyEarlyCareerDevelopmentAward($11,500),2008.InstitutionalNomineeforPackardFoundationFellowship,2007.BrownCenterforComputationalMolecularBiology,ScholarshipInnovatorAward($5000),2007.Namedone“Tomorrow’sPI’s”byGenomeTechnologymagazine,2006.BurroughsWellcomeCareerAwardattheScientificInterface,2005-2010.IntelligentSystemsinMolecularBiology(ISMB),BestPosterAward,2005.AlfredP.SloanFoundation/DOEFellowshipinComputationalBiology,2002-04.U.S.DepartmentofEducation,GAANNFellowshipinMathematics(declined),1999.TEACHINGEnrollmentsindicatedin[]


2012-2015 Instructor,“CSCI1810:ComputationalMolecularBiology.”Fall2015[34],

Fall2014[14],Fall2013[27];Fall2012[42];Spring2012[23]2007-2015 Instructor(andcoursecreator)“CSCI2950-C:TopicsinComputational

Biology:Genomes,Networks,andCancer.”Spring2015[9];Spring2013[6];Fall2011[12];Fall2010[7];Fall2009[6];Fall2008,Fall2007,Spring2006.

2008,2011 Instructorfor“CSCI0220:IntroductiontoDiscreteMathematics,”acorecourseforCSconcentrators.Spring2011[86];Spring2008[67].

2009-2011 Guestlecturesfor“BIOL2010:QuantitativeApproachesinBiology.”2009 Designedandtaughtnewcourse“CSCI1950-Z:ComputationalMethodsfor

Biology.”Spring2009[14].2006-presentReadingandResearch(Graduate):Spring2015[5];Fall2014[4];Spring

2014[3];Fall2013[4];Spring2013[5];Fall2012[5];Spring2012[6];Fall2011[6];Spring2011[2],Fall2010[3];Spring2010;Fall2009;Spring2009;Fall2008;Spring2008;Fall2007;Spring2007.

2007-presentIndividualIndependentStudy(Undergraduate):Spring2015[1];Fall2014[1];Spring2014[6];Fall2013[2];Fall2012[2];Spring2012[1],Fall2011[3],Spring2011[1],Fall2010[1];Spring2010;Fall2009;Spring2009;Fall2008;Spring2008;Fall2007;Spring2007;Fall2006.

1996-2002 TeachingAssistant,DepartmentofMathematics,UniversityofCalifornia,SanDiego.Fouryearsofexperienceleadingweeklydiscussionsectionsinundergraduatecoursesincluding:Calculus,DifferentialEquations,LinearAlgebra,andIntroductiontoAlgorithms.

1996 Lecturer,MassachusettsInstituteofTechnology.DesignedandtaughtintersessioncourseIntroductiontoMathematicalProofswithHenryCohn.

AdvisingBrownUniversity,ProvidenceRIPh.D.StudentsResearchSupervisor:

1. ThomasSchaffner,2016-present.2. AshleyConard,2015-present.[RecipientofNSFGraduateResearchFellowship(2015-)3. RebeccaElyanow,2015-present.4. GryteSatas,2014-present.[HonorableMention,NSFGraduateResearchFellowship(2015)]5. MaxLeiserson,2011-2016.[Ph.D.completed,May2016][RecipientofNSFGraduateResearch

Fellowship(2012-2014)]6. Hsin-TaWu,2010-2016.[Ph.D.completed,May2016]7. LaylaOesper,2010-2015.[Ph.D.completed,May2015][RecipientofNSFGraduateResearch

Fellowship(2011-2013).RecipientofGoogleAnitaBorgMemorialScholarship2014].8. AhmadMahmoody,2011-2013.CompletedSc.M.9. MatthewParks[withChipLawrence],2011-2014.[Ph.D.completed,May2014]10. AlexandraPapoutsaki,2011-2013.CompletedSc.M.11. FabioVandin,2008-2010.[VisitingPh.D.studentfromUniversityofPadova]12. AnnaRitz,2006-2012.[Ph.D.completed,Oct.2012][RecipientofNSFGraduateResearch

Fellowship(2008-2011)]


13. CrystalKahn,2007-2010.[Ph.D.completed,Oct.2010][RecipientofNSFGraduateResearchFellowship(2005-2008)]

PostdoctoralFellows:

1. DoraErdos,2015-2016.2. MohammedEl-Kebir,2014-present.3. MatthewReyna,2014-present.4. ImanHajirasouliha,2013-2014.[RecipientofNSERCPostdoctoralFellowship,2014]5. JasonDobson,2013-2014.6. FabioVandin,2010-2013.7. SuzanneSindi,2006-2012.

Master’sStudentsResearchSupervisor:

1. JeremyWatson,2014-present2. JohnShen,Sc.M.,December2015.3. JonathanEldridge,Sc.M.,Dec.2014.4. Hsin-TaWu,Sc.M.,May2010.5. BorislavHristov,Sc.M.,May2010.6. SelimOnal,Sc.M.,May2010.7. BrendanHickey,Sc.M,May2009.8. EricLim,Sc.MDecember2007.

Ph.D.Thesiscommittees:

WilliamJordan(MolecularBiology,CellBiology,andBiochemistry),2016-present.ConnorGramazio(ComputerScience),2015-present.PriyankaNakka(ComputationalBiology),2014-present.MichaelHughes(ComputerScience),2014-present.ChristineScaduto(MolecularBiology,CellBiology,andBiochemistry),2012-present

JohnUrban(MolecularBiology,CellBiology,andBiochemistry),2012-2016.StevenCriscione(MolecularBiology,CellBiology,andBiochemistry),2012-2016.WenjinZhou(ComputerScience),2009-2012.

JadrianMiles(ComputerScience),2009-2016. RaduJianu(ComputerScience),2009-2012.

LuisCarvalho(AppliedMathematics),2007-2008.

Ph.D.ResearchExamCommitteesKamranAzam(ComputerScience),2008.

Ph.D.AdvisoryCommittees PriyankaNakka(ComputationalBiology),2014.

YinghongLan(EcologyandEvolutionaryBiology),2012.Master’sStudentAdvising: CaoRen,2015-present. BrigitteHarder,2013-2015. AaronShen,2010-2011.


UndergraduateAdvising

• HonorsTheses:HannahAcheson-Field(2015),VivianHsiao(2014),VisheshJain(2014),JovianYu(2012),ElenaHelman(2009)

• ConcentrationAdvisorforComputationalBiology.(2008-present)• ConcentrationAdvisorforComputerScience.(2007-present)• SophomoreAdvisingProgram.(2009-present).• SeniorCapstoneprojects:JihanChao(2010),BrendanHickey(2008)andPeter

Goldstein(2008).• HonorsTheses(Reader):WilliamStephanson(2015),AaronBehr(2015),Glen

Scheinberg(EEB),2008.UniversityofCalifornia,SanDiegoUndergraduateResearchMentoring

SarahAerni(2005-2006).[FinalistforComputingResearchAssociation’sOutstandingUndergraduateAwardProgram,2006]

Documents

BENJAMIN J. RAPHAEL - Brown Universitycompbio-research.cs.brown.edu/people/BRaphael_CV.pdf · Dr. Benjamin J. Raphael C.V., January 2017. Page 1 of 23 BENJAMIN J. RAPHAEL Professor