2025
scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links
Wang G, Zhao J, Lin Y, Liu T, Zhao Y, Zhao H. scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links. Nature Communications 2025, 16: 4994. PMID: 40442129, PMCID: PMC12122792, DOI: 10.1038/s41467-025-60333-z.Peer-Reviewed Original ResearchConceptsDeep learning frameworkSingle-cell multi-omics researchSingle-cell multi-omics dataLearning frameworkMulti-omics dataGenerative adversarial networkSingle-cell technologiesData alignmentSingle-cell resolutionMulti-omics researchDownstream analysisCellular statesOmics datasetsAdversarial networkNeural networkProteomic profilingCorrelated featuresBiological informationOmics perspectiveDiverse datasetsFeature topologyDisease mechanismsCell embeddingData resourcesRelationship inferenceA multi-omic approach implicates novel protein dysregulation in post-traumatic stress disorder
Wang J, Liu Y, Li H, Nguyen T, Soto-Vargas J, Wilson R, Wang W, Lam T, Zhang C, Lin C, Lewis D, Glausier J, Holtzheimer P, Friedman M, Williams K, Picciotto M, Nairn A, Krystal J, Duman R, Young K, Zhao H, Girgenti M. A multi-omic approach implicates novel protein dysregulation in post-traumatic stress disorder. Genome Medicine 2025, 17: 43. PMID: 40301990, PMCID: PMC12042318, DOI: 10.1186/s13073-025-01473-1.Peer-Reviewed Original ResearchConceptsPost-traumatic stress disorderDorsolateral prefrontal cortexPsychiatric disordersAutism spectrum disorderPrefrontal cortexDepressive disorderStress disorderGamma-aminobutyric acidGenome-wide association studiesPTSD brainsGenome-wide measurementsStudies of postmortem brainsSubgenual prefrontal cortexDisabling psychiatric disorderMultiple psychiatric disordersPrefrontal cortical areasPTSD casesHuman brain studiesBrain regionsSpectrum disorderGABAergic processesPostmortem brainsMDDProtein co-expression modulesProteomic profilingThe left amygdala is genetically sexually-dimorphic: multi-omics analysis of structural MRI volumes
Gui Y, Zhou G, Cui S, Li H, Lu H, Zhao H. The left amygdala is genetically sexually-dimorphic: multi-omics analysis of structural MRI volumes. Translational Psychiatry 2025, 15: 17. PMID: 39843917, PMCID: PMC11754786, DOI: 10.1038/s41398-025-03223-8.Peer-Reviewed Original ResearchConceptsLeft amygdala volumePolygenic risk scoresLeft amygdalaSex differencesBrain volumeMental disordersAmygdala volumeBrain anatomyEffect of polygenic risk scoresStudy of sex differencesExamined sex differencesPsychiatric Genomics ConsortiumMechanisms of sex differencesSex-specific genetic correlationsGenetic correlation analysisAmygdalaStructural MRI volumesSexually-dimorphicGenetic correlationsBrainDisordersRNA-seq dataGenomics ConsortiumCell-type compositionKnowledge of genetic basis
2023
Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression
Ruan P, Todd J, Zhao H, Liu Y, Vinisko R, Soellner J, Schmid R, Kaner R, Luckhardt T, Neely M, Noth I, Porteous M, Raj R, Safdar Z, Strek M, Hesslinger C, Palmer S, Leonard T, Salisbury M. Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression. Respiratory Research 2023, 24: 141. PMID: 37344825, PMCID: PMC10283254, DOI: 10.1186/s12931-023-02435-0.Peer-Reviewed Original ResearchMeSH KeywordsDisease ProgressionFemaleHumansIdiopathic Pulmonary FibrosisLungMaleMicroRNAsMultiomicsProteomicsConceptsComposite physiologic indexProgression-free survivalTransplant-free survivalMolecular subtypesSubtype 1Risk groupsProspective registrySubtype 2Disease progressionProspective registry of patientsIPF-PRO RegistryB-cell receptor signalingBackgroundIdiopathic pulmonary fibrosisRegistry of patientsCox proportional hazards modelsIntegrative multi-omics analysisAccumulation of extracellular matrixProportional hazards modelTransplant-freeProgression-FreeMolecular endotypesEnrichment of clinical trialsAntifibrotic treatmentMulti-omics analysisPulmonary fibrosis
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