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 levelSequenceUnveiling 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 splittingGenesNovel heterozygous SPI1c.538C>T p.(Leu180Phe) variant causes PU.1 haploinsufficiency leading to agammaglobulinemia
Daddali R, Kettunen K, Turunen T, Knox A, Laine P, Chowdhury I, Vänttinen M, Mamia N, Stiegler A, Boggon T, Kere J, Romberg N, Seppänen M, Varjosalo M, Martelius T, Grönholm J. Novel heterozygous SPI1c.538C>T p.(Leu180Phe) variant causes PU.1 haploinsufficiency leading to agammaglobulinemia. Clinical Immunology 2025, 277: 110503. PMID: 40294836, DOI: 10.1016/j.clim.2025.110503.Peer-Reviewed Original ResearchConceptsDendritic cell countHeterozygous loss-of-function variantsLoss-of-function variantsCentrosome-associated proteinsFamily transcription factorsEts family transcription factorGene expression patternsAssociated with B cell developmentHematopoietic cell fatePDC countsB cell developmentCell countDisrupts gene expression patternsB-cell countsCell fateCarrier sisterSevere bacterial infectionsTranscription factorsIsolated IgA deficiencyFinnish familiesExpression patternsIn vitro studiesIgA deficiencyVariable penetranceIndex patientHSPA2 influences the differentiation and production of immunomodulatory mediators in human immortalized epidermal keratinocyte lines
Gogler A, Wilk A, Sojka D, Adamiec-Organiściok M, Matysiak N, Kania D, Wiecha K, Małusecka E, Cortez A, Zamojski D, Marczyk M, Mazurek A, Oziębło S, Scieglinska D. HSPA2 influences the differentiation and production of immunomodulatory mediators in human immortalized epidermal keratinocyte lines. Cell Death & Disease 2025, 16: 344. PMID: 40287440, PMCID: PMC12033329, DOI: 10.1038/s41419-025-07565-5.Peer-Reviewed Original ResearchConceptsChaperone proteinsKeratinocyte differentiationCell type-specific expression patternsHomologous chaperone proteinsEpidermal keratinocyte differentiationInterferon-mediated signalingInterferon-stimulated genesControl proteostasisExtracellular secretionTranscriptome analysisMolecular machineryKeratinocyte differentiation markersHSPA2Upper epidermal layersDifferentiation defectsExpression patternsSomatic cellsMolecular networksPro-inflammatory IL-6 cytokinePotential therapeutic targetFunctional analysisSecretion of IL-6Keratinocyte linePathogenic factorsReduced levelsBatch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Millard N, Chen J, Palshikar M, Pelka K, Spurrell M, Price C, He J, Hacohen N, Raychaudhuri S, Korsunsky I. Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. Genome Biology 2025, 26: 36. PMID: 40001084, PMCID: PMC11863647, DOI: 10.1186/s13059-025-03479-9.Peer-Reviewed Original ResearchConceptsBatch effectsVisualization of gene expression patternsSpatial gene patternsGene expression analysis of cellsGene expression patternsGene expression analysisGene expression levelsGene colocalizationAnalysis of cellsGene patternsTranscriptome analysisLigand-receptor interactionsExpression patternsSpatial transcriptomicsSpatial transcriptomic analysisExpression levelsGenesMultiple samplesSpatial patternsTranscriptomeColocalizationAnatomical contextPatternsCount data
2024
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis
Liu T, Long W, Cao Z, Wang Y, He C, Zhang L, Strittmatter S, Zhao H. CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. Briefings In Bioinformatics 2024, 26: bbae626. PMID: 39592241, PMCID: PMC11596696, DOI: 10.1093/bib/bbae626.Peer-Reviewed Original ResearchEvolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum
Marshall K, Stadtmauer D, Maziarz J, Wagner G, Lesch B. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum. Developmental Cell 2024, 60: 646-664.e8. PMID: 39536760, PMCID: PMC11859772, DOI: 10.1016/j.devcel.2024.10.013.Peer-Reviewed Original ResearchPlacental mammalsLevel of transcriptionSingle-cell dataGene expression patternsMammalian spermatogenesisGene expression programsEpigenomic dataAdult testisEvolutionary innovationSpermatogenic cellsGene setsSpermatogenic developmentModel marsupialOpossum Monodelphis domesticaGene expressionExpression patternsGenesDevelopmental processesExpression programsSpermatogenesisMonodelphis domesticaMammalsDevelopmental timeCombination of featuresExpressionTranscriptional regulation of postnatal aortic development
Weiss D, Yeung N, Ramachandra A, Humphrey J. Transcriptional regulation of postnatal aortic development. Cells And Development 2024, 180: 203971. PMID: 39426523, PMCID: PMC11634634, DOI: 10.1016/j.cdev.2024.203971.Peer-Reviewed Original ResearchSelective utilization of glucose metabolism guides mammalian gastrulation
Cao D, Bergmann J, Zhong L, Hemalatha A, Dingare C, Jensen T, Cox A, Greco V, Steventon B, Sozen B. Selective utilization of glucose metabolism guides mammalian gastrulation. Nature 2024, 634: 919-928. PMID: 39415005, PMCID: PMC11499262, DOI: 10.1038/s41586-024-08044-1.Peer-Reviewed Original ResearchConceptsCellular metabolismMammalian gastrulationHexosamine biosynthetic pathwayTranscription factor networksCellular signaling pathwaysSignaling morphogensGlucose metabolismCellular programmeBiosynthetic pathwayFate acquisitionCell fateHousekeeping natureGenetic mechanismsMesoderm migrationFactor networksERK activationExpression patternsSignaling pathwayDevelopmental processesStem cell modelCell typesSpecialized functionsDevelopmental contextMammalian embryosMouse embryosProteomic basis for pancreatic acinar cell carcinoma and pancreatoblastoma as similar yet distinct entities
Tanaka A, Ogawa M, Zhou Y, Hendrickson R, Miele M, Li Z, Klimstra D, Wang J, Roehrl M. Proteomic basis for pancreatic acinar cell carcinoma and pancreatoblastoma as similar yet distinct entities. Npj Precision Oncology 2024, 8: 221. PMID: 39363045, PMCID: PMC11449907, DOI: 10.1038/s41698-024-00708-5.Peer-Reviewed Original ResearchAcinar cell carcinomaPancreatic ductal adenocarcinomaActin-based processesPathway activity differencesCell carcinomaChromosome organizationChromosomal proteinsProteomic basisRNA processingIGF2 pathwayProtein expression patternsEpithelial-to-mesenchymal transitionProteogenomic profilingPancreatic acinar cell carcinomaProteomic landscapeDNA repairCell cycleRare pancreatic malignancyExpression patternsMitochondrial dysfunctionStem cell phenotypeMetabolic adaptationProteinExtracellular matrixPancreatic malignancyCC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow
Kim A, Sakin I, Viviano S, Tuncel G, Aguilera S, Goles G, Jeffries L, Ji W, Lakhani S, Kose C, Silan F, Oner S, Kaplan O, Group M, Ergoren M, Mishra-Gorur K, Gunel M, Sag S, Temel S, Deniz E. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Science Alliance 2024, 7: e202402708. PMID: 39168639, PMCID: PMC11339347, DOI: 10.26508/lsa.202402708.Peer-Reviewed Original ResearchConceptsDevelopmental disabilitiesIntellectual disabilityPatient-derived fibroblastsMidbrain regionsBrain developmentDefective ciliogenesisCSF circulationDisabilityCSF flowAbnormal CSF flowNervous system developmentMutant tadpolesCiliated tissuesMultiple model systemsVariant functionPronephric ductUnrelated familiesCC2D1AExpression patternsCiliogenesisRenal dysplasiaLeft-right organizerFunctional analysisDisease mechanismsBrainHEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics
Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nature Communications 2024, 15: 5700. PMID: 38972896, PMCID: PMC11228050, DOI: 10.1038/s41467-024-49846-1.Peer-Reviewed Original ResearchConceptsSpatially variable genesVariable genesSpatial expression patternsSpatial transcriptomics technologiesSpatial transcriptomics researchTranscriptome researchTranscriptomic technologiesBiological functionsExpression patternsSpatial transcriptomicsGenesState-of-the-art methodsColorectal cancer dataHeterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling
Ohashi Y, Protack C, Aoyagi Y, Gonzalez L, Thaxton C, Zhang W, Kano M, Bai H, Yatsula B, Alves R, Hoshina K, Schneider E, Long X, Perry R, Dardik A. Heterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling. Scientific Reports 2024, 14: 13287. PMID: 38858395, PMCID: PMC11164895, DOI: 10.1038/s41598-024-64075-8.Peer-Reviewed Original ResearchConceptsGene expression patternsArteriovenous fistula groupArteriovenous fistulaExpression patternsHeterogeneous gene expressionGene expression changesOutcomes of arteriovenous fistulaVenous remodelingArteriovenous fistula maturationPostoperative day 7Reduce patient morbidityRNA sequencingUpregulation of metabolismBioinformatics analysisGene expressionDownregulation of metabolismMetabolic pathwaysExpression changesGenesAVF maturationAVF remodelingFistula creationC57BL/6 miceClinical outcomesPatient morbidityInvestigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts
Itai T, Yan F, Liu A, Dai Y, Iwaya C, Curtis S, Leslie E, Simon L, Jia P, Chen X, Iwata J, Zhao Z. Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts. Human Genetics And Genomics Advances 2024, 5: 100313. PMID: 38807368, PMCID: PMC11318074, DOI: 10.1016/j.xhgg.2024.100313.Peer-Reviewed Original ResearchDe novo variantsCPO geneOMIM genesGene functionScRNA-seq data analysisOrofacial cleftsMan (OMIMScRNA-seq analysisOnline Mendelian InheritanceSingle-cell RNA sequencingSingle-cell expression profilesInvestigate gene functionCleft palateScRNA-seqGene setsCellular expression profilesMendelian inheritanceGenetic variantsRNA sequencingOrofacial clefting genesContextual geneGenesExpression patternsCongenital birth defectsExpression profilesProperties and predicted functions of large genes and proteins of apicomplexan parasites
Fang T, Mohseni A, Lonardi S, Mamoun C. Properties and predicted functions of large genes and proteins of apicomplexan parasites. NAR Genomics And Bioinformatics 2024, 6: lqae032. PMID: 38584870, PMCID: PMC10993292, DOI: 10.1093/nargab/lqae032.Peer-Reviewed Original ResearchApicomplexan parasitesCausative agent of toxoplasmosisProtein sizeAgent of toxoplasmosisPathogen-host interactionsToxoplasma gondii</i>Conventional metabolic pathwaysCompact genomeEukaryotic organismsEncode proteinsEvolutionary constraintsNutrient acquisitionApicomplexan pathogensEvolutionary pressureAntigenic variationMetabolic pathwaysExpression patternsLarger proteinsParasitesCausative agentProteinGenesImmune evasionErythrocyte invasionPlasmodium falciparum</i>Vascular development, remodeling and maturation
Furtado J, Eichmann A. Vascular development, remodeling and maturation. Current Topics In Developmental Biology 2024, 159: 344-370. PMID: 38729681, DOI: 10.1016/bs.ctdb.2024.02.001.Peer-Reviewed Original ResearchGene expression patternsKnowledge of vascular biologyControlling nutrient uptakeEarly embryonic developmentDysfunctional vasculatureVascular systemVascular system developmentSystem dysfunctionExpression patternsOrgan physiologyFunctional circulatory systemEndothelial cellsTherapeutic potentialEmbryonic developmentVascular system dysfunctionNutrient uptakeBlood vesselsSemi-permeable barrierVascular biologyHuman morbidityLive imaging of Fibronectin 1a-mNeonGreen and Fibronectin 1b-mCherry knock-in alleles during early zebrafish development
Jülich D, Holley S. Live imaging of Fibronectin 1a-mNeonGreen and Fibronectin 1b-mCherry knock-in alleles during early zebrafish development. Cells And Development 2024, 177: 203900. PMID: 38218338, PMCID: PMC10947920, DOI: 10.1016/j.cdev.2024.203900.Peer-Reviewed Original ResearchKnock-in alleleECM fibersLoss of function phenotypesGenetic complementation experimentsAdhesion receptor familyComplementation experimentsDouble mutantLive in vivo imagingExtracellular matrix glycoproteinFibronectin matrixPosterior hindgutPresomitic mesodermZebrafish developmentExpression patternsMRNA injectionIntegrinLive imagingCross-regulationAllelesFibronectinReceptor familyParaxial mesodermCo-localizationExtracellular matrixMutants
2023
ML Based Phenotype Analysis Using Differential Gene Expression Data in Schizophrenia
D A, KJ S, Maniappan V, B S, S D, R P, Raja K, Oviya I. ML Based Phenotype Analysis Using Differential Gene Expression Data in Schizophrenia. 2023, 00: 1-7. DOI: 10.1109/icstcee60504.2023.10585167.Peer-Reviewed Original ResearchGene expression dataGene expression patternsGene expression profilesGene orientationSNP informationExpression dataGene expressionPhenotypic analysisExpression patternsGenesExpression profilesCell phenotypeBiological mechanismsBiological mechanisms of schizophreniaMechanisms of schizophreniaEqtnSNPsTherapeutic approachesPhenotypeSodium currents in naïve mouse dorsal root ganglion neurons: No major differences between sexes
Ghovanloo M, Tyagi S, Zhao P, Effraim P, Dib-Hajj S, Waxman S. Sodium currents in naïve mouse dorsal root ganglion neurons: No major differences between sexes. Channels 2023, 18: 2289256. PMID: 38055732, PMCID: PMC10761158, DOI: 10.1080/19336950.2023.2289256.Peer-Reviewed Original ResearchConceptsSexual dimorphismRodent dorsal root ganglion neuronsBiophysical propertiesDorsal root ganglion neuronsExpression patternsSex-dependent regulationVoltage-gated sodiumFunctional analysisGanglion neuronsRodent sensory neuronsMouse dorsal root ganglion neuronsNaïve WT miceNumber of cellsMixed populationDimorphismUniform experimental conditionsSex-dependent differencesSensory neuronsNative DRG neuronsPain pathwaysDRG neuronsWT miceClinical studiesNav currentsAdult malesEndothelial nitric oxide synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation
Nguyen T, Rahman N, Sessa W, Lee M. Endothelial nitric oxide synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation. Frontiers In Cardiovascular Medicine 2023, 10: 1279868. PMID: 38034389, PMCID: PMC10683645, DOI: 10.3389/fcvm.2023.1279868.Peer-Reviewed Original ResearchAtherosclerotic plaque formationPlaque formationAkt1 null miceSingle amino acid substitutionMutant miceLesion formationImportance of AktUnique expression patternGene expression analysisIndex of atherosclerosisFavorable lipid profileVascular protective roleAtherosclerotic lesion formationAthero-protective effectsEndothelial NO generationAmino acid substitutionsDouble knockout miceDeletion backgroundPhosphorylation sitesAspartate substitutionPhosphorylation statusExpression analysisEnzyme functionExpression patternsENOS deletion
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