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Research Scientist
Appointments
Education & Training
- Non Degree Program
- The Jackson Laboratory for Genomic Medicine, Postdoctoral Associate (2021)
- PhD
- Dartmouth College, Experimental and Molecular Medicine (2016)
- BS
- University of Massachusetts Amherst (2011)
Research
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Overview
Dr. Kevin Johnson is a Research Scientist in Professor Roel Verhaak's laboratory with a strong background in cancer genomics, epigenetics, and glioma evolution. In the Verhaak Lab, he leads computational analyses of multi-modal bulk and single cell longitudinal genomic data to better understand glioma treatment resistance. Dr. Johnson has a proven track record of producing high-quality research including first or co-first author publications in scientific journals such as Nature, Nature Genetics, and Nature Communications. He is also an active research member in (inter)national scientific consortium such as the Glioma Longitudinal AnalySiS (GLASS) consortium that investigates brain tumor molecular evolution and the Participant Engagement and Cancer Genome Sequencing (PE-CGS) consortium that directly engages patients in cancer genomics research.
ORCID
0000-0003-0016-5158
Research at a Glance
Yale Co-Authors
Frequent collaborators of Kevin Johnson's published research.
Publications Timeline
A big-picture view of Kevin Johnson's research output by year.
Roel Verhaak, PhD
Samir Amin
Elizabeth Claus, PhD, MD
22Publications
2,113Citations
Publications
2025
Engagement Methods in Brain Tumor Genomic Research: Multimethod Comparative Study
DeCamp M, Barnard J, Ritger C, Helmkamp L, Begum A, Garcia-Hernandez S, Fischmann R, Gay N, Gonzalez-Fisher R, Johnson K, Lennox L, Lipof G, Ostmeyer J, Perkins I, Pyle L, Salmi L, Thompson T, Claus E, Verhaak R, Kwan B. Engagement Methods in Brain Tumor Genomic Research: Multimethod Comparative Study. Journal Of Participatory Medicine 2025, 17: e68852. PMID: 40839870, PMCID: PMC12411796, DOI: 10.2196/68852.Peer-Reviewed Original ResearchAltmetricConceptsEngagement methodsAdvisory CouncilQualitative content analysisCare partnersOptimal engagementParticipants' experiencesRegistry researchParticipant engagementUnique participantsQualitative findingsTweet chatsResearch Advisory CouncilPositive experiencesContent analysisParticipantsEngagement activitiesDiverse perspectivesGenomic researchDiverse backgroundsEngagementFacebook discussionsSurveyRecommendationsCareRegistryThe multilayered transcriptional architecture of glioblastoma ecosystems
Nomura M, Spitzer A, Johnson K, Garofano L, Nehar-belaid D, Galili Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, ChowdhFury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Verhaak R, Iavarone A, Suvà M, Tirosh I. The multilayered transcriptional architecture of glioblastoma ecosystems. Nature Genetics 2025, 57: 1155-1167. PMID: 40346361, PMCID: PMC12081307, DOI: 10.1038/s41588-025-02167-5.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCell typesSingle-nucleus RNA sequencingDiversity of cellular statesMalignant cell statesGene expression programsTumor DNA sequencingDNA sequencesTranscriptional architectureCellular statesTranscriptional heterogeneityRNA sequencingCell statesCellular heterogeneityExpression programsGenetic aberrationsRecurrent GBM samplesPathway activationLayer of heterogeneityNeuronal-likeNonmalignant cell typesGBM samplesTherapeutic resistanceSequenceEcosystemCell-likeDeciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics
Spitzer A, Johnson K, Nomura M, Garofano L, Nehar-belaid D, Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, Chowdhury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Iavarone A, Verhaak R, Tirosh I, Suvà M. Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. Nature Genetics 2025, 57: 1168-1178. PMID: 40346362, PMCID: PMC12081298, DOI: 10.1038/s41588-025-02168-4.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSingle-cell genomicsSingle-nucleus RNA sequencingMalignant cell statesDNA sequencesNeuronal cell typesTumor microenvironmentRNA sequencingMalignant cell fractionCell statesCell typesCell fractionIsocitrate dehydrogenase (IDH)-wildtype glioblastomaStandard-of-care therapyCo-evolutionMolecular heterogeneityTumor microenvironment modifierEcosystemTumor microenvironment compositionSubsets of patientsSequenceRecurrent glioblastoma
2024
Mapping extrachromosomal DNA amplifications during cancer progression
Kim H, Kim S, Wade T, Yeo E, Lipsa A, Golebiewska A, Johnson K, An S, Ko J, Nam Y, Lee H, Kang S, Chung H, Niclou S, Moon H, Paek S, Bafna V, Luebeck J, Verhaak R. Mapping extrachromosomal DNA amplifications during cancer progression. Nature Genetics 2024, 56: 2447-2454. PMID: 39402156, PMCID: PMC11549044, DOI: 10.1038/s41588-024-01949-7.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPretreatment tumorsCancer progressionChemotherapy-pretreated patientsNewly diagnosed tumorsVariant allele fractionUntreated metastasesPrimary cancerUntreated cancerTreatment responseFocal amplificationTumor samplesChromosomal amplificationsDiagnosed cancerTumorExtrachromosomal DNA amplificationsAdvanced cancerCancerEcDNATime pointsMetastasisNewlyDNA amplificationProgressionExtrachromosomal DNAPatients
2023
The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen
Malta T, Sabedot T, Morosini N, Datta I, Garofano L, Vallentgoed W, Varn F, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan J, Gan H, Hasanain M, Hau A, Johnson K, Cazacu S, deCarvalho A, Khasraw M, Kocakavuk E, Kouwenhoven M, Migliozzi S, Niclou S, Niers J, Ormond D, Paek S, Reifenberger G, Smitt P, Smits M, Stead L, van den Bent M, Van Meir E, Walenkamp A, Weiss T, Weller M, Westerman B, Ylstra B, Wesseling P, Lasorella A, French P, Poisson L, Woehrer A, Lowman A, deCarvalho A, Castro A, Transou A, Brodbelt A, Hau A, Lasorella A, Golebiewska A, Walenkamp A, Molinaro A, Iavarone A, Ismail A, Westerman B, Ylstra B, Bock C, Ormond D, Brat D, Kocakavuk E, Van Meir E, Barthel F, Varn F, D'Angelo F, Finocchiaro G, Rao G, Zadeh G, Reifenberger G, ngNg H, Kim H, Noushmehr H, Miletic H, Gan H, Datta I, Rock J, Snyder J, Huse J, Connelly J, Barnholtz-Sloan J, Niers J, deGroot J, Akdemir K, Kannan K, Ligon K, Aldape K, Bulsara K, Johnson K, Alfaro K, Poisson L, Garofano L, Stead L, Nasrallah M, Smits M, van den Bent M, Kouwenhoven M, Weller M, Hasanain M, Khasraw M, Gould P, Smitt P, LaViolette P, Tatman P, Wesseling P, French P, Beroukhim R, Verhaak R, Migliozzi S, Niclou S, Bakas S, Kalkanis S, Paek S, Short S, Ghazaleh T, Malta T, Sabedot T, Weiss T, Walbert T, Baid U, Vallentgoed W, Yung W, Verhaak R, Iavarone A, Noushmehr H. The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen. Cancer Research 2023, 84: 741-756. PMID: 38117484, PMCID: PMC10911804, DOI: 10.1158/0008-5472.can-23-2093.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsIDHmut gliomasIDHmut tumorsIDHwt gliomasResponse to therapeutic pressureGenes associated with tumor progressionT cell infiltrationLevels of global methylationIDH1 mutation statusAssociated with survivalDNA methylationLoss of DNA methylationGenome-wide DNA methylationRecurrent tumorsIncreased neoangiogenesisMutation statusIDH-wildtypeTherapy resistanceHistological progressionTherapeutic pressureLevel of genome-wide DNA methylationTumor microenvironmentT cellsTreatment regimenTumor adaptationIDH-mutant
2022
EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY
Johnson K, Anderson K, Nehar-Belaid D, Varn F, Gujar A, Courtois E, Robson P, Moon H, Golebiewska A, Paek S, Niclou S, Verhaak R. EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY. Neuro-Oncology 2022, 24: vii118-vii118. PMCID: PMC9660532, DOI: 10.1093/neuonc/noac209.448.Peer-Reviewed Original ResearchConceptsSingle-nucleus RNATranscription factorsCellular heterogeneityCell state plasticityEpigenetic gene regulationOpen chromatin stateOpen chromatin peaksWhole-genome sequencing dataDynamic epigenetic alterationsDNA methylation studiesGenome sequencing dataPatient-derived cell linesChromatin stateChromatin accessibilityEpigenetic switchChromatin changesGene regulationTranscriptional changesStem-like cellsMaster regulatorCell statesCell diversityEpigenetic alterationsEnhancer regionSequencing dataGlioma progression is shaped by genetic evolution and microenvironment interactions
Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R, Consortium T, Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Alfaro K, Amin S, Ashley D, Bock C, Brodbelt A, Bulsara K, Castro A, Connelly J, Costello J, de Groot J, Finocchiaro G, French P, Golebiewska A, Hau A, Hong C, Horbinski C, Kannan K, Kouwenhoven M, Lasorella A, LaViolette P, Ligon K, Lowman A, Mehta S, Miletic H, Molinaro A, Ng H, Niclou S, Niers J, Phillips J, Rabadan R, Rao G, Reifenberger G, Sanai N, Short S, Smitt P, Sloan A, Smits M, Snyder J, Suzuki H, Tabatabai G, Tanner G, Tomaszewski W, Wells M, Westerman B, Wheeler H, Xie J, Yung W, Zadeh G, Zhao J, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022, 185: 2184-2199.e16. PMID: 35649412, PMCID: PMC9189056, DOI: 10.1016/j.cell.2022.04.038.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSpecific ligand-receptor interactionsMicroenvironment interactionsDNA sequencing dataGlioma progressionLigand-receptor interactionsNeoplastic cellsSignaling programsCell statesSequencing dataGenetic evolutionGenetic changesIDH wild-type tumorsIsocitrate dehydrogenaseMesenchymal transitionSomatic alterationsDistinct mannerActive tumor growthIDH-mutant gliomasPotential targetTherapy resistanceAdult patientsDisease progressionPossible roleCellsTumor growthLive-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Yi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jillette N, Clow P, Cheng A, Verhaak R. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discovery 2022, 12: 468-483. PMID: 34819316, PMCID: PMC8831456, DOI: 10.1158/2159-8290.cd-21-1376.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsExtrachromosomal DNA elementsDNA elementsUneven segregationRNA polymerase IILive-cell imagingPolymerase IIOffspring cellsGene transcriptionCell line modelsEcDNAsRandom segregationGenetic materialLiving cellsCopy numberLive cellsIndividual cellsTumor evolutionMitosisInheritance patternBreakpoint sequencesIssue featureTranscriptionFluorescent markersPatient tissuesCells
2021
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response
Johnson K, Anderson K, Courtois E, Gujar A, Barthel F, Varn F, Luo D, Seignon M, Yi E, Kim H, Estecio M, Zhao D, Tang M, Navin N, Maurya R, Ngan C, Verburg N, de Witt Hamer P, Bulsara K, Samuels M, Das S, Robson P, Verhaak R. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nature Genetics 2021, 53: 1456-1468. PMID: 34594038, PMCID: PMC8570135, DOI: 10.1038/s41588-021-00926-8.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsBrain NeoplasmsCell PlasticityClonal EvolutionDNA Copy Number VariationsDNA MethylationEpigenesis, GeneticGene Expression Regulation, NeoplasticGenetic HeterogeneityGenome, HumanGliomaHumansMutationPhylogenyPromoter Regions, GeneticSingle-Cell AnalysisStress, PhysiologicalTumor MicroenvironmentConceptsDNA methylation disorderEnvironmental stress responsesMethylation disordersEnvironmental stress response pathwaysStress responseStress response processesStress response pathwaysSingle-cell transcriptomesDNA methylation changesDNA methylation differencesDNA methylation dataMulti-omics profilesDNA methylomeTranscriptional disruptionEpigenetic instabilityEpigenetic heterogeneityEpigenetic regulatorsResponse pathwaysCellular plasticityMethylation changesMethylation differencesCell statesMethylation dataIrradiation stressWild-type gliomasSerum cell-free DNA epigenetic biomarkers aid glioma diagnostics and monitoring
Johnson K, Verhaak R. Serum cell-free DNA epigenetic biomarkers aid glioma diagnostics and monitoring. Neuro-Oncology 2021, 23: 1423-1424. PMID: 34139018, PMCID: PMC8408867, DOI: 10.1093/neuonc/noab146.Peer-Reviewed Original ResearchCitations
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