2025
Precision multiplexed base editing in human cells using Cas12a-derived base editors
Schweitzer A, Adams E, Nguyen M, Lek M, Isaacs F. Precision multiplexed base editing in human cells using Cas12a-derived base editors. Nature Communications 2025, 16: 5061. PMID: 40449999, PMCID: PMC12126522, DOI: 10.1038/s41467-025-59653-x.Peer-Reviewed Original ResearchConceptsMultiplex base editingBase editingBase editorsBase editor variantsMammalian genome engineeringBase editing technologyGenome engineering technologiesDNA double strand breaksBase editing systemMammalian genomesDouble strand breaksMultiple lociPolygenic phenotypesHuman cell linesHuman genomeGenome engineeringTarget nucleotideEditing outcomesMutation rateMultiplex editingMultiple gRNAsHuman cellsExpression cassetteEditing technologyGenomeCell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs
Ward T, Qu P, Leung L, Zhou B, Muench K, Khechaduri A, Plastini M, Charlton C, Pattni R, Ho S, Ho M, Huang Y, Zhou P, Hallmayer J, Mourrain P, Palmer T, Zhang X, Urban A. Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs. European Journal Of Human Genetics 2025, 1-10. PMID: 40374944, DOI: 10.1038/s41431-025-01856-3.Peer-Reviewed Original ResearchCopy number variantsDNA methylation patternsGlobal reprogrammingMethylation patternsInduced pluripotent stem cellsNeuropsychiatric copy number variantsGene expressionDifferentially expressed genesInduced neuronsCell-type specific alterationsGenome-wideDNA methylomeDuplicate genotypingHuman genomeGene familyLocal genomesDNA methylationInduced pluripotent stem cell lineGenesMolecular etiologyDNAGenomePluripotent stem cellsProtocadherinTranscriptomeThe retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity
Wood T, Henriques W, Cullen H, Romero M, Blengini C, Sarathy S, Sorkin J, Bekele H, Jin C, Kim S, Wang X, Laureau R, Chemiakine A, Khondker R, Isola J, Stout M, Gennarino V, Mogessie B, Jain D, Schindler K, Suh Y, Wiedenheft B, Berchowitz L. The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity. Nature Aging 2025, 5: 765-779. PMID: 40263616, PMCID: PMC12180178, DOI: 10.1038/s43587-025-00852-y.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesTranscription factor MYBL1Gonadal tissueMale gonadal tissueRNA intermediateEvolutionary innovationHuman genomeAssociation studiesHost genomeProtein self-assemblyDevelopmental regulationCapsid geneCapsid-like structuresHuman cellsCapsid formationYears ago4,5RetrotransposonsGenomeSequenceGenesRNAReproductive capacityPNMA1Reproductive functionMouse modelEukaryotic Microproteins
Jaunbocus N, Ebenki V, Su H, Slavoff S. Eukaryotic Microproteins. Annual Review Of Biochemistry 2025, 94: 1-28. PMID: 40245354, PMCID: PMC12207985, DOI: 10.1146/annurev-biochem-080124-012840.Peer-Reviewed Original ResearchA compendium of human gene functions derived from evolutionary modelling
Ramsey J, Siegele D, Chisholm R, Fey P, Giglio M, Nadendla S, Antonazzo G, Attrill H, Brown N, Garapati P, Marygold S, Ahmed S, Asanitthong P, Buitrago D, Erdol M, Gage M, Huang S, Kadhum M, Li K, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu S, Su R, Xu Q, Lovering R, Blake J, Christie K, Corbani L, Dolan M, Ni L, Sitnikov D, Smith C, Lera-Ramirez M, Rutherford K, Wood V, D’Eustachio P, Demos W, De Pons J, Dwinell M, Hayman G, Kaldunski M, Kwitek A, Laulederkind S, Smith J, Tutaj M, Vedi M, Wang S, Engel S, Karra K, Miyasato S, Nash R, Skrzypek M, Weng S, Wong E, Achsel T, Andres-Alonso M, Bagni C, Bayés À, Biederer T, Brose N, Chua J, Coba M, Cornelisse L, de Juan-Sanz J, Goldschmidt H, Gundelfinger E, Huganir R, Imig C, Jahn R, Jung H, Kaeser P, Kim E, Koopmans F, Kreutz M, Lipstein N, MacGillavry H, McPherson P, O’Connor V, Pielot R, Ryan T, Sala C, Sheng M, Smalla K, Smit A, Toonen R, van Weering J, Verhage M, Verpelli C, Bakker E, Berardini T, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter M, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Famiglietti M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin M, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Chan J, Diamantakis S, Raciti D, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. A compendium of human gene functions derived from evolutionary modelling. Nature 2025, 640: 146-154. PMID: 40011791, PMCID: PMC11964926, DOI: 10.1038/s41586-025-08592-0.Peer-Reviewed Original ResearchHuman gene functionHuman protein-coding genesProtein-coding genesGene functionFunctional repertoireGene Ontology enrichment analysisGene Ontology ConsortiumOntology enrichment analysisHuman genomeHuman genesEvolutionary timeEvolutionary originGenomic techniquesEvolutionary modeling approachExpert-curatedEnrichment analysisGenesRegulatory functionsFunctional characteristicsEvolutionary modelsBiomedical researchGenomeRepertoireOrganisms1,2Body of informationGestational trophoblastic disease: STR genotyping for precision diagnosis
Rozenova K, Buza N, Hui P. Gestational trophoblastic disease: STR genotyping for precision diagnosis. Expert Review Of Molecular Diagnostics 2025, 25: 1-19. PMID: 39801212, DOI: 10.1080/14737159.2025.2453506.Peer-Reviewed Original ResearchConceptsShort tandem repeatsGestational trophoblastic diseaseShort tandem repeat genotypingDiagnosis of gestational trophoblastic diseaseGestational trophoblastic tumorsHydatidiform MoleSTR genotypingTrophoblastic tumorDifferential diagnosis of gestational trophoblastic diseaseRepetitive DNA sequencesManagement of gestational trophoblastic diseaseSubclassification of hydatidiform molesGestational trophoblastic neoplasmsPrognostication of patientsPaternity testingNon-neoplastic natureHuman genomeTandem repeatsDNA sequencesForensic identityTrophoblastic diseaseTrophoblastic neoplasmsGynecologic conditionsDiagnostic workupClinical outcomes
2024
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
Li C, Bonder M, Syed S, Jensen M, Consortium H, Group H, Gerstein M, Zody M, Chaisson M, Talkowski M, Marschall T, Korbel J, Eichler E, Lee C, Shi X. An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Research 2024, 34: 2304-2318. PMID: 39638559, PMCID: PMC11694747, DOI: 10.1101/gr.279419.124.Peer-Reviewed Original ResearchConceptsTopologically associating domainsTopologically associating domains boundariesImpact of structural variantsLymphoblastoid cell linesStructural variantsHuman genomeGene regulationAdjacent TADsHuman lymphoblastoid cell linesCell linesSub-TADGenomic structureInsulate genesChromatin architectureImpact of deletionChromatin structureGenomeAberrant regulationAnalysis pipelineMammalian speciesGenesCCREsFunctional impactChromatinRegulationExpression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity
Aldrovandi S, Castro J, Ullrich K, Karger A, Luria V, Tautz D. Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity. Genome Biology And Evolution 2024, 16: evae175. PMID: 39663928, PMCID: PMC11635099, DOI: 10.1093/gbe/evae175.Peer-Reviewed Original ResearchConceptsOpen reading frameGene open reading frameCellular regulatory pathwaysNoncoding DNAReading frameHuman cell linesHuman genomeAlpha-helicesGrowth experimentsCellular physiologyFunctional diversityPositive selectionBeta-sheetTranscriptomic responseRegulatory pathwaysAdaptive advantageHuman cellsGenesCell clonesCell linesSequenceClonesRandom sequencePathwayCellsMachine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cells80. IMPLICATION OF COMPLEX STRUCTURAL GENOME VARIATION IN THE GENETIC ARCHITECTURE OF NEUROPSYCHIATRIC DISORDERS: INSIGHTS FROM HUMAN POPULATION ANALYSIS AND FROM POSTMORTEM BRAINS OF INDIVIDUALS WITH PSYCHIATRIC DISORDERS
Zhou B, Arthur J, Guo H, Kim T, Huang Y, Pattni R, Song G, Palejev D, Dohna H, Roussos P, Kundaje A, Hallmayer J, Snyder M, Wong, Urban A. 80. IMPLICATION OF COMPLEX STRUCTURAL GENOME VARIATION IN THE GENETIC ARCHITECTURE OF NEUROPSYCHIATRIC DISORDERS: INSIGHTS FROM HUMAN POPULATION ANALYSIS AND FROM POSTMORTEM BRAINS OF INDIVIDUALS WITH PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2024, 87: 93. DOI: 10.1016/j.euroneuro.2024.08.194.Peer-Reviewed Original ResearchWhole-genome sequencingComplex structural variationsHuman genomeMarker SNPsContinental populationsRisk allelesShort-read whole-genome sequencingSingle-nuclei RNA-seqFunctional genomics dataComplex genetic architectureDNA sequence variantsComplex genetic componentPost-mortem brainsPopulation-scale studiesDifferentially expressed genesVariant typeIntegration of genotypesStructural variationsGWAS lociGenome biologyCandidate lociIndividual genomesLinkage analysisGenomic analysisGenomic dataDetection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
Zhou B, Arthur J, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo J, Lee H, Nachun D, Purmann C, Monte E, Weimer A, Qu P, Shi M, Jiang L, Yang X, Fullard J, Bendl J, Girdhar K, Kim M, Chen X, Consortium P, Greenleaf W, Duncan L, Ji H, Zhu X, Song G, Montgomery S, Palejev D, Dohna H, Roussos P, Kundaje A, Hallmayer J, Snyder M, Wong H, Urban A. Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell 2024, 187: 6687-6706.e25. PMID: 39353437, PMCID: PMC11608572, DOI: 10.1016/j.cell.2024.09.014.Peer-Reviewed Original ResearchComplex structural variationsNatural human genetic variationHuman genetic variationCell type-specific expressionHuman-specific evolutionDifferential gene expressionStructural variationsContinental populationsChromatin accessibilityHuman genomeGenetic variationNeural genesGenomeGene expressionRisk allelesMolecular etiologyCell typesGenesPostmortem brainsChromatinLociAllelesMachine-learning-based methodsMultiomicsBrain regionsResolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints
Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer S, Roychowdhury T, Wood R, Ho M, Dohna H, Abyzov A, Hallmayer J, Wong W, Ji H, Urban A. Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2322834121. PMID: 39042694, PMCID: PMC11295037, DOI: 10.1073/pnas.2322834121.Peer-Reviewed Original ResearchConceptsLong-read sequencingPulse-field gel electrophoresisBase-pair resolutionDNA methylation patternsCell-type specific analysisCell type-specificChromosomal interactionsSequence assemblySegmental duplicationsGenome sequenceGenomic rearrangementsGenomic regionsChromosomal breakpointsHuman genomeGenomic recombinationMethylation patternsSequence analysisHaplotype-specificDeletion haplotypesGel electrophoresisGenomeAmplification-freeBreakpoint locationsMicrodeletion disorderType-specificA comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Du Z, He J, Jiao W. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25: 91. PMID: 38589937, PMCID: PMC11003132, DOI: 10.1186/s13059-024-03239-1.Peer-Reviewed Original ResearchConceptsPlant genomesGenotyping methodsComplexity of plant genomesHeterozygous plant genomesGenotypic algorithmsGenotype millionsShort readsGenomic contextGenomic diversitySequencing technologiesHuman genomeGenomeGenetic variantsExcessive repeatsVariant typeGenotypesStructural variationsEnsemble pipelinePlantsConclusionsOur studyVariant genotypesGenotype performanceVariantsDeletionSequenceGenetics of liver disease in adults
Konkwo C, Chowdhury S, Vilarinho S. Genetics of liver disease in adults. Hepatology Communications 2024, 8: e0408. PMID: 38551385, PMCID: PMC10984672, DOI: 10.1097/hc9.0000000000000408.Peer-Reviewed Original ResearchConceptsInterpretation of genetic variationNext-generation sequencing technologiesIncorporation of genomic informationSomatic genetic variantsGenomic informationSequencing technologiesHuman genomeLiver diseaseGenetic variationGenetic variantsImprove patient careMonogenic diseasesProtective allelesPersonalized medicinePatient careManagement of patientsChronic liver diseaseContribution of riskHealth problemsAnnual deathsGlobal health problemHepatology practiceGenomeEstimated 2AllelesFibrotic cocktail treated human precision lung slices replicate the cellular diversity of the IPF lung
Justet A, Pineda H, Adams T, Balayev A, Mitash N, Ishizuka M, Kim H, Khoury J, Cala-García J, Flint J, Schupp J, Ahangari F, Yan X, Rosas I, Kaminski N, Königshoff M. Fibrotic cocktail treated human precision lung slices replicate the cellular diversity of the IPF lung. Revue Des Maladies Respiratoires 2024, 41: 218. DOI: 10.1016/j.rmr.2024.01.074.Peer-Reviewed Original ResearchCellular repertoireCell typesSingle cell platformsSequence readsCDNA libraryIllumina platformHuman genomeNucleus transcriptomicsCellular diversityIPF lungsPulmonary fibrosisEMT markersAirway epithelial cellsBasaloid cellsCellular populationsEpithelial cellsFibrotic fibroblastsCell platformLung slicesLung cell populationsHuman precision-cut lung slicesCell populationsSenescence markersCellsBasal markers
2023
Leveraging base-pair mammalian constraint to understand genetic variation and human disease
Sullivan P, Meadows J, Gazal S, Phan B, Li X, Genereux D, Dong M, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas M, Marinescu V, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins L, Lawler A, Keough K, Zheng Z, Zeng J, Wray N, Li Y, Johnson J, Chen J, Paten B, Reilly S, Hughes G, Weng Z, Pollard K, Pfenning A, Forsberg-Nilsson K, Karlsson E, Lindblad-Toh K, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023, 380: eabn2937. PMID: 37104612, PMCID: PMC10259825, DOI: 10.1126/science.abn2937.Peer-Reviewed Original ResearchConceptsHuman genomeHuman diseasesCopy-number variationsHeritable human diseasesGenome annotationVariant annotationGenomic positionsGenomic regionsDisease heritabilityFunctional annotationEvolutionary constraintsAssociation studiesCopy-numberGenetic variationGenetic findingsGenomeCell typesRegulatory landscapeDisease mechanismsAnnotationBiological mechanismsCancer dataMammalsPredictor of functionHeritabilityEvolutionary constraint and innovation across hundreds of placental mammals
Christmas M, Kaplow I, Genereux D, Dong M, Hughes G, Li X, Sullivan P, Hindle A, Andrews G, Armstrong J, Bianchi M, Breit A, Diekhans M, Fanter C, Foley N, Goodman D, Goodman L, Keough K, Kirilenko B, Kowalczyk A, Lawless C, Lind A, Meadows J, Moreira L, Redlich R, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown A, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev S, Lawler A, Marinescu V, Morrill K, Osmanski A, Paulat N, Phan B, Reilly S, Schäffer D, Steiner C, Supple M, Wilder A, Wirthlin M, Xue J, Birren B, Gazal S, Hubley R, Koepfli K, Marques-Bonet T, Meyer W, Nweeia M, Sabeti P, Shapiro B, Smit A, Springer M, Teeling E, Weng Z, Hiller M, Levesque D, Lewin H, Murphy W, Navarro A, Paten B, Pollard K, Ray D, Ruf I, Ryder O, Pfenning A, Lindblad-Toh K, Karlsson E, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023, 380: eabn3943. PMID: 37104599, PMCID: PMC10250106, DOI: 10.1126/science.abn3943.Peer-Reviewed Original ResearchConceptsEncyclopedia of DNA ElementsProtein-coding exonsUltraconserved elementsGenome functionGenomic resourcesOrganismal phenotypesDNA elementsFunctional annotationEvolutionary constraintsHuman genomeRegulatory elementsMammalian traitsGenomeGenetic variantsPlacental mammalsTherapeutic developmentMammalsSpeciesDisease riskExonGenesBiodiversityPhenotypeTraitsRepeatsAn atlas of substrate specificities for the human serine/threonine kinome
Johnson J, Yaron T, Huntsman E, Kerelsky A, Song J, Regev A, Lin T, Liberatore K, Cizin D, Cohen B, Vasan N, Ma Y, Krismer K, Robles J, van de Kooij B, van Vlimmeren A, Andrée-Busch N, Käufer N, Dorovkov M, Ryazanov A, Takagi Y, Kastenhuber E, Goncalves M, Hopkins B, Elemento O, Taatjes D, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry S, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck P, Turk B, Yaffe M, Cantley L. An atlas of substrate specificities for the human serine/threonine kinome. Nature 2023, 613: 759-766. PMID: 36631611, PMCID: PMC9876800, DOI: 10.1038/s41586-022-05575-3.Peer-Reviewed Original ResearchConceptsSer/ThrHuman Ser/ThrSubstrate specificityPhosphorylation eventsProtein serine/threonine kinaseWidespread post-translational modificationSerine/threonine kinasePutative protein kinaseSubstrate sequence specificityIntrinsic substrate specificityPost-translational modificationsThreonine phosphorylationGenetic perturbationsThreonine kinasePhosphorylation sitesHuman genomeProtein phosphorylationProtein kinaseSequence specificityBiological pathwaysHuman diseasesNegative selectivityKinaseUnexpected insightsKinome
2022
Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeR
Mandell J, Cannataro V, Townsend J. Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeR. Cancer Research 2022, 83: 500-505. PMID: 36469362, PMCID: PMC9929515, DOI: 10.1158/0008-5472.can-22-1508.Peer-Reviewed Original ResearchConceptsMutation rateEpistatic effectsSite-specific mutation ratesNeutral mutation rateNucleotide mutation ratePan-cancer datasetCancer cell survivalFunctional impact scoresCustom genomesPairwise epistasisSet of variantsHuman genomeR packageTranscriptomic dataSomatic variant dataModel of selectionSingle nucleotideCancer effectsCell survivalNucleotide mutationsCancer biologyVariant dataMutational signature analysisMutationsSomatic mutationsUBXN3B Controls Immunopathogenesis of Arthritogenic Alphaviruses by Maintaining Hematopoietic Homeostasis
Geng T, Yang D, Lin T, Cahoon J, Wang P. UBXN3B Controls Immunopathogenesis of Arthritogenic Alphaviruses by Maintaining Hematopoietic Homeostasis. MBio 2022, 13: e02687-22. PMID: 36377866, PMCID: PMC9765034, DOI: 10.1128/mbio.02687-22.Peer-Reviewed Original ResearchConceptsUbiquitin regulatory X domain-containing proteinDomain-containing proteinsDiverse cellular processesCell-intrinsic mannerCellular processesHematopoietic homeostasisPhysiological functionsRNA virus replicationEssential roleControl of infectionChikungunya virusHuman genomeArthritogenic alphavirusesImmune responseCHIKV replicationDNA virusesRNA virusesInnate immune responseVirus-specific immunoglobulin GO'nyong'nyong virusLong-term neurological disordersSignificant public health problemSerum cytokine levelsSpecific antiviral drugsHigh viral load
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