2025
Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data
Zhang H, Jiang Z, Zhang S, Tu L, Carlson D. Scale-free and unbiased transformer with tokenization for cell type annotation from single-cell RNA-seq data. Pattern Recognition 2025, 168: 111724. DOI: 10.1016/j.patcog.2025.111724.Peer-Reviewed Original ResearchSingle-cell RNA-seq dataHigh-throughput single-cell RNA sequencingGene pathway informationCell type annotationRNA-seq dataSingle-cell datasetsSingle-cell RNA sequencingGene expression vectorScRNA-seqPathway informationDiverse speciesRNA sequencingExpression vectorAnnotation methodGene expressionDropout eventsExpression patternsGenesSpeciesType annotationsAnnotationCellsComprehensive intra-Cell levelSequenceSurvey and Improvement Strategies for Gene Prioritization with Large Language Models
Neeley M, Qi G, Wang G, Tang R, Mao D, Liu C, Pasupuleti S, Yuan B, Xia F, Liu P, Liu Z, Hu X. Survey and Improvement Strategies for Gene Prioritization with Large Language Models. Bioinformatics Advances 2025, vbaf148. DOI: 10.1093/bioadv/vbaf148.Peer-Reviewed Original ResearchProtocol to implement saturation mutagenesis-reinforced functional assays to resolve small-sized variants in disease-related genes
Gauthier L, Wang Z, Ng K, Huang S, Mao Y, Lek M, Ma K. Protocol to implement saturation mutagenesis-reinforced functional assays to resolve small-sized variants in disease-related genes. STAR Protocols 2025, 6: 103909. PMID: 40540392, DOI: 10.1016/j.xpro.2025.103909.Peer-Reviewed Original ResearchDisease-related genesDisease-causing genetic variantsFluorescence-based cell sortingNext-generation sequencingFunctional assaysDisease genesAllelic seriesSaturation mutagenesisGenetic variantsGenesFunctional impactCell sortingHigh-throughputVariantsDisease fieldAssayMutagenesisSequenceCellsNucleofectionSortingGenetics of Response to ECT, TMS, Ketamine and Esketamine
Franklin C, Altinay M, Bailey K, Bhati M, Carr B, Conroy S, Khurshid K, McDonald W, Mickey B, Murrough J, Nestor S, Nickl‐Jockschat T, Reti I, Sanacora G, Trapp N, Viswanath B, Wright J, Zandi P, Potash J. Genetics of Response to ECT, TMS, Ketamine and Esketamine. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2025, e33038. PMID: 40525674, DOI: 10.1002/ajmg.b.33038.Peer-Reviewed Original ResearchGenome-wide association studiesSingle nucleotide polymorphismsTreatment responseEffects of variantsElectroconvulsive therapyGenetic predictors of treatment responseTreatment modalitiesAssociation studiesCandidate genesFactors affecting treatment responseAssociated with treatment responseResponse to available treatmentsGene studiesNucleotide polymorphismsTreatment-resistant mood disordersGenetic predictors of responseTreatment-resistant depressionPredictors of treatment responsePredictors of responseGroup of patientsGenesTranscranial magnetic stimulationGeneticsGenetic predictorsClinical responseEnergetics of Whole Genome Doubling and Genomic Instability
Beck R, Tagal V, Amin S, Bakhoum S, Maley C, Verhaak R, Gomes A, Andor N. Energetics of Whole Genome Doubling and Genomic Instability. Cancer Letters 2025, 217878. PMID: 40517938, DOI: 10.1016/j.canlet.2025.217878.Peer-Reviewed Original ResearchWhole-genome doublingGenome doublingBuffering deleterious mutationsDeleterious mutationsHaploinsufficient genesGenomic instabilityGenomic alterationsEnergetic constraintsTime of diagnosisCancer cellsMutationsPloidyCancer researchTissue sitesCancerAneuploidyTime of detectionGenomeCellsGenesShed lightIdentification of F-box proteins in ABA- and GA-regulated seed germination: interaction of GASA1 signalling peptide and ABA-induced ubiquitination
Kasera M, Ceciliato P, Lopez B, Hauser F, Gendron J, Schroeder J. Identification of F-box proteins in ABA- and GA-regulated seed germination: interaction of GASA1 signalling peptide and ABA-induced ubiquitination. Philosophical Transactions Of The Royal Society B Biological Sciences 2025, 380: 20240233. PMID: 40439299, PMCID: PMC12121378, DOI: 10.1098/rstb.2024.0233.Peer-Reviewed Original ResearchConceptsSeed germinationSignal peptideGenetic screeningF-box proteinsForward genetic screensHomology-based gene silencingInhibition of seed germinationABA-insensitiveHomologous genesFunctional genomicsGene familyTriple mutantF-boxABA inhibitionProteasome pathwayAmiRNA linesGene silencingInteraction partnersGerminating seedsArtificial microRNAGenesABAGerminationMutantsUbiquitinPossible role of mosaic mutations of neurodevelopmental disorder-related genes in bipolar disorder: Lessons from Kmt2c chimeric heterozygous knockout mice
Nakamura T, Nakajima K, Fujimori-Tonou N, Kasahara T, Tsuboi T, Kato T. Possible role of mosaic mutations of neurodevelopmental disorder-related genes in bipolar disorder: Lessons from Kmt2c chimeric heterozygous knockout mice. Neuroscience Research 2025, 217: 104910. PMID: 40414358, DOI: 10.1016/j.neures.2025.05.005.Peer-Reviewed Original ResearchBipolar disorderSpectrum of bipolar disordersAutism-like phenotypeAutism spectrum disorderAutism-like behaviorsDepression-like episodesKnockout miceMosaic mutationsHeterozygous knockout miceMental disordersSpectrum disorderKleefstra syndromeGenetic architecture of bipolar disorderDisordersSymptomatic spectrumAnxietyExome sequencing analysisGenetic architectureSequence analysisCausative genesMosaic miceGenesSomatic mutationsAutismKMT2CUnveiling the shared etiology between gastrointestinal disorders and valvular heart diseases through a genome-wide pleiotropy study
Xu J, Liu Z, Wu L, Pei F, Jiang H, Cheng C, Yang W, Yuan J, Polimanti R, Yang Y. Unveiling the shared etiology between gastrointestinal disorders and valvular heart diseases through a genome-wide pleiotropy study. Npj Cardiovascular Health 2025, 2: 17. DOI: 10.1038/s44325-025-00054-w.Peer-Reviewed Original ResearchLinkage disequilibrium score regressionGenetic correlationsPleiotropic analysisPleiotropy analysisGut microbiotaGenetic pathwaysMicrobial influenceScore regressionPleiotropic effectsGenetic linkPathwayHeart diseaseButyricicoccusMicrobiotaGenesGutComposite null hypothesisVariantsGastrointestinal disordersCausal effectsLinkageDiseaseIBDETS emerges to heat up adipose
Rodeheffer M. ETS emerges to heat up adipose. Genes & Development 2025 PMID: 40389324, DOI: 10.1101/gad.352966.125.Peer-Reviewed Original ResearchTranscription factor bindingE26 transformation-specific (ETS) transcription factorsPromoter chromatin accessibilityChromatin accessibilityFactor bindingTranscription factorsHistone acetylationAdipose biologyGene expressionETV4HistoneTranscriptionGenesUCP1AcetylationE26AdipogenesisBindingBiologyThermogenesisExpressionAdiposeAlternative splicing across the C. elegans nervous system
Weinreb A, Varol E, Barrett A, McWhirter R, Taylor S, Courtney I, Basavaraju M, Poff A, Tipps J, Collings B, Krishnaswamy S, Miller D, Hammarlund M. Alternative splicing across the C. elegans nervous system. Nature Communications 2025, 16: 4508. PMID: 40379606, PMCID: PMC12084653, DOI: 10.1038/s41467-025-58293-5.Peer-Reviewed Original ResearchConceptsAlternative splicingNeuronal genesDifferential alternative splicingNervous system of Caenorhabditis elegansC. elegans nervous systemSplicing regulatory networkUNC-40/DCCRNA featuresRegulatory networksSAX-3/RoboSplicing patternsCaenorhabditis elegansSplicingGene expressionGenesNeuronal identityNeuron typesWeb interfaceNervous systemMicroexonsTranscriptomeElegansRNANeuronsCell-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 cellsProtocadherinTranscriptomeDynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry
Mohsen H, Blenman K, Emani P, Morris Q, Carrot-Zhang J, Pusztai L. Dynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry. BMC Medical Genomics 2025, 18: 87. PMID: 40375077, PMCID: PMC12082885, DOI: 10.1186/s12920-025-02154-z.Peer-Reviewed Original ResearchConceptsGenomic variationGenomic cohortsStudy of human genomic variationWhole exome sequencing datasetsTrait-specific lociHuman genomic variationCancer-relevant genesGenomic patternsGenomic signalsGenomic studiesSequencing datasetsCancer typesGermline variantsDisease predispositionBiological processesFunctional analysisGeographic scalesPhenotypic continuumClustering patternsPotential driversDiverse data collectionsRace categoriesLociGenesComplete portraitCoarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci
Mader A, Rodriguez A, Yuan T, Surovtsev I, King M, Mochrie S. Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci. Biophysical Journal 2025, 124: 2120-2132. PMID: 40369871, DOI: 10.1016/j.bpj.2025.05.008.Peer-Reviewed Original ResearchChromatin polymerChromatin configurationLocus identityGenomic positionsLabeled lociLiving cellsLocus configurationsChromatin dynamicsMultiple lociGene locusChromatin researchChromatinLociSingle-particle trackingFluorescent labelingCorrect assignmentDynamic loopTemporal dynamicsCellsGenesModel polymersLabelingIdentityAssociation of clinical manifestations and immune alterations with genetic variants of uncertain significance in patients concerned for inborn errors of immunity
Novotny S, Yoo N, Chen J, Granoth M, Kohli-Pamnani A, Hsu F, Rodenas M, Steele R, Kaman K, Soffer G, Price C, Kuster J, Kang I, Osmani L, Shin J. Association of clinical manifestations and immune alterations with genetic variants of uncertain significance in patients concerned for inborn errors of immunity. Clinical Immunology 2025, 277: 110513. PMID: 40354868, DOI: 10.1016/j.clim.2025.110513.Peer-Reviewed Original ResearchInborn errors of immunityErrors of immunityGenetic variantsInborn errorsAssociation of clinical manifestationsGene clusterGene functionStudy evaluated associationsImmune alterationsDiagnostic challengeClinical manifestationsImmunological profileGenetic testingVUSGenesImmunological characteristicsImmune functionLaboratory dataImmunityVariantsAssociationPatientsNew dimensions in the molecular genetics of insect chemoreception
Talross G, Carlson J. New dimensions in the molecular genetics of insect chemoreception. Trends In Genetics 2025 PMID: 40340097, DOI: 10.1016/j.tig.2025.04.003.Peer-Reviewed Original ResearchMolecular geneticsChemosensory systemOdorant receptor genesRNA editingChemoreceptor expressionInsect chemoreceptionEpigenetic mechanismsLong noncoding RNAsOlfactory receptor neuronsNoncoding RNAsMolecular componentsReceptor geneTaste receptorsRNAReceptor neuronsChemoreceptionDrosophilaGenesNew insightsInsectsSpread diseaseThe application of irreversible genomic states to define and trace ancient cell type homologies
Simakov O, Wagner G. The application of irreversible genomic states to define and trace ancient cell type homologies. EvoDevo 2025, 16: 5. PMID: 40319312, PMCID: PMC12049793, DOI: 10.1186/s13227-025-00242-w.Peer-Reviewed Original ResearchImpact gene expressionGenomic stateCell typesGene expressionGene regulatory networksHomologous cell typesBranching animalsGenomic charactersRegulatory elementsRegulatory networksRegulatory signaturesMorphological traitsHomologyPhenotypic levelMolecular signaturesOntogenetic originGenesMorphological featuresNon-functionalCellsHypothesis articleGenomeExpressionTraitsTypeUnveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST
Gong Y, Yuan X, Jiao Q, Yu Z. Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST. Nature Communications 2025, 16: 3977. PMID: 40295488, PMCID: PMC12037780, DOI: 10.1038/s41467-025-59139-w.Peer-Reviewed Original ResearchConceptsGene expression signalsSpatial transcriptomics data analysisExpression signalsTranscriptome data analysisHeterogeneous graph networkReal-world datasetsSpatial expression patternsOver-smoothing problemSpatial transcriptomics dataGlobal spatial relationshipsST data analysisTranscriptome dataUltra-large-scaleConquer strategyExpression patternsGraph networkData splittingGenesAn abundance of aliC and aliD genes were identified in saliva using a novel multiplex qPCR to characterize group II non-encapsulated pneumococci with improved specificity.
Laxton C, Toekiran F, Lin T, Lomeda B, Hislop M, Keller L, Allicock O, Wyllie A. An abundance of aliC and aliD genes were identified in saliva using a novel multiplex qPCR to characterize group II non-encapsulated pneumococci with improved specificity. Microbiology 2025, 171 PMID: 40279151, DOI: 10.1099/mic.0.001555.Peer-Reviewed Original ResearchConceptsBioinformatics analysisMultiplex qPCRGenome sequenceGenetic exchangeCapsule genesCps regionPolymicrobial samplesIsolated coloniesNon-pneumococcal streptococciPublished primersSpecies specificityMolecular methodsQPCR assayEncapsulated strainsGenesAntimicrobial resistancePneumococcal surveillance studiesMultiplex assayScreening salivaAssayStreptococciSequenceIsolatesColoniesPneumococcal carriageThe 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 modelEmerging roles of transcriptional condensates as temporal signal integrators
Meyer K, Huang B, Weiner O. Emerging roles of transcriptional condensates as temporal signal integrators. Nature Reviews Genetics 2025, 1-12. PMID: 40240649, DOI: 10.1038/s41576-025-00837-y.Peer-Reviewed Original ResearchGene regulatory networksTranscriptional condensatesRegulatory networksControl cell physiologyTemporal signal integrationMethod to probeSignaling networksSignaling specificityCell physiologyGene activationTranscription factorsSignaling dynamicsBiophysical frameworkSignal adaptationTranscriptionGenesSignalDecoding mechanismSignal integrityFrequency of signalsPhysiologyMechanism
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