Declan Clarke, PhD
Associate Research ScientistCards
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Associate Research Scientist
Appointments
Molecular Biophysics and Biochemistry
Associate Research ScientistPrimary
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Education & Training
- PhD
- Yale University (2016)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of Declan Clarke's published research.
Publications Timeline
A big-picture view of Declan Clarke's research output by year.
Alexej Abyzov, PhD
Duy Phan, PhD
9Publications
229Citations
Publications
2021
A novel signature predicts recurrence risk and therapeutic response in breast cancer patients
Tran QH, Than VT, Luu PL, Clarke D, Lam HN, Nguyen T, Nguyen D, Duy PQ, Phung D, Nguyen MN. A novel signature predicts recurrence risk and therapeutic response in breast cancer patients. International Journal Of Cancer 2021, 148: 2848-2856. PMID: 33586202, DOI: 10.1002/ijc.33512.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAcetylserotonin O-MethyltransferaseBreast NeoplasmsDatabases, GeneticFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansNeoplasm GradingOligonucleotide Array Sequence AnalysisRetrospective StudiesSequence Analysis, RNASurvival AnalysisTamoxifenTreatment OutcomeUp-RegulationConceptsBreast cancer patientsAcetylserotonin O-methyltransferaseEndocrine therapyCancer patientsASMT expressionRelapse-free survival outcomesMetastasis-free survival timeLonger metastasis-free survival timesLow-risk casesBreast cancer progressionBreast cancer tumorsAdjuvant chemotherapyOverall survivalTamoxifen treatmentEndocrine resistanceDistance recurrenceMRNA array dataRetrospective studySurvival outcomesTherapeutic responseBreast cancerSurvival timePatientsRecurrence riskSynthesis of melatonin
2018
Network Analysis as a Grand Unifier in Biomedical Data Science
McGillivray P, Clarke D, Meyerson W, Zhang J, Lee D, Gu M, Kumar S, Zhou H, Gerstein M. Network Analysis as a Grand Unifier in Biomedical Data Science. Annual Review Of Biomedical Data Science 2018, 1: 1-28. DOI: 10.1146/annurev-biodatasci-080917-013444.Peer-Reviewed Original ResearchCitationsAltmetric
2016
Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation
Clarke D, Sethi A, Li S, Kumar S, Chang RW, Chen J, Gerstein M. Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure 2016, 24: 826-837. PMID: 27066750, PMCID: PMC4883016, DOI: 10.1016/j.str.2016.03.008.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAllosteric residuesIntra-species conservationEvolutionary time scalesDisease-associated variantsProtein conformational changesSelective constraintsAllosteric hotspotsSequencing initiativesOwn proteinsInformation-flow bottlenecksDeep sequencingConformational changesDisease locusBiophysical reasonsResiduesSurface pocketsConservationAllosteryLociSequencingProteinHotspotsPocketPDBVariants
2015
Reads meet rotamers: structural biology in the age of deep sequencing
Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Current Opinion In Structural Biology 2015, 35: 125-134. PMID: 26658741, PMCID: PMC4751031, DOI: 10.1016/j.sbi.2015.11.003.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsStructural biologyPersonal genome sequencesHuman populationSequence conservationCommon foldNovel foldGenome sequenceProtein interactionsDeep sequencingLarge complexesBiologySequenceStructure databaseSpeciesSequencingProteinFoldsReadsConservationPopulationGreater fractionComplexesDiscoveryVast amountStructure
2013
Localized structural frustration for evaluating the impact of sequence variants
Kumar S, Clarke D, Gerstein M. Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Research 2013, 44: 10062-10073. PMID: 27915290, PMCID: PMC5137452, DOI: 10.1093/nar/gkw927.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSingle nucleotide variantsTumor suppressor geneRare single nucleotide variantsPopulation-scale sequencingSomatic single nucleotide variantsDisease-related single nucleotide variantsPhenotype-genotype associationsLocalized frustrationProtein stabilityFunction eventsProtein structureSuppressor geneProtein databankSequence variantsProtein functionalityCommon variantsOncogeneRelated variantsLocal interactionsOpposite patternVariantsGenomeDeleteriousnessGenesSequencing
2012
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012, 28: 2267-2269. PMID: 22743228, PMCID: PMC3426844, DOI: 10.1093/bioinformatics/bts368.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCloud-computing environmentVariant annotation toolsAmazon Machine ImageCommand line interfaceLarge data filesMachine imagesWeb servicesVirtual machinesDemand accessWeb applicationSource codeAnnotation toolData filesComputational frameworkPersonal genomesDifferent variantsGenomic coordinatesSimple intersectionDetailed documentationPHPMachineSequencing projectsAnnotationEnvironmentFilesNovel insights through the integration of structural and functional genomics data with protein networks
Clarke D, Bhardwaj N, Gerstein MB. Novel insights through the integration of structural and functional genomics data with protein networks. Journal Of Structural Biology 2012, 179: 320-326. PMID: 22343087, PMCID: PMC4830681, DOI: 10.1016/j.jsb.2012.02.001.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsWide protein-protein interaction networkProtein-protein interaction networkFunctional genomics dataProtein-protein interactionsMacromolecular structural dataCellular processesBiological organizationInteraction networksProtein networkGenomic dataSystems biologyProtein structureConstituent proteinsEvolutionary featuresMacromolecular structure determinationNovel insightsSilico predictionPredictive frameworkGraph modelStructural dataRespective functionsBiological featuresStructure determinationIntrinsic differencesStatic nodes
2011
Systematic control of protein interactions for systems biology
Bhardwaj N, Clarke D, Gerstein M. Systematic control of protein interactions for systems biology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20279-20280. PMID: 22160691, PMCID: PMC3251072, DOI: 10.1073/pnas.1118084109.Peer-Reviewed Original ResearchCitationsAltmetricIntegration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsMulti-interface hubsMolecular networksConformational changesInteraction networksTransient interactionsStructural interaction networksProtein interaction networksClassification of proteinsDynamic conformational changesProtein structural featuresSmall conformational changesTransient associationGene expressionMore plasticityProtein motionsStructural databankProteinAlternate conformationDifferent mechanismsDrastic structural changesDomainInteraction