2025
Bayesian Longitudinal Network Regression With Application to Brain Connectome Genetics
Li C, Tian X, Gao S, Wang S, Wang G, Zhao Y, Zhao Y. Bayesian Longitudinal Network Regression With Application to Brain Connectome Genetics. Statistics In Medicine 2025, 44: e70069. PMID: 40277222, DOI: 10.1002/sim.70069.Peer-Reviewed Original ResearchConceptsSample relatednessLongitudinal genome-wide association studiesGenome-wide association studiesBrain imaging genetic studiesMultivariate phenotypesGenetic signalsImaging genetics studiesAssociation studiesGenetic studiesGenetic variantsGenetic underpinningsGenetic contributionGenetic effectsRelatednessAdolescent Brain Cognitive DevelopmentBrain functional connectivityFunctional organizationBiological architectureFunctional connectivityRobust inferenceGeneticsPhenotypeAnalytical challengesPosterior inferenceBrain network configurationModularity Measures of Functional Brain Networks Predict Individual Differences in Long‐Term Memory
Zhou M, Chun M, Lin Q. Modularity Measures of Functional Brain Networks Predict Individual Differences in Long‐Term Memory. European Journal Of Neuroscience 2025, 61: e70052. PMID: 40091538, DOI: 10.1111/ejn.70052.Peer-Reviewed Original ResearchConceptsLong-term memoryPredicting individual differencesRecollection memoryIndividual differencesBrain networksLong-term memory performanceLong-term memory capacityMeasures of brain activityBrain functional organizationBrain functional connectivityMode networkBrain activityFunctional connectivityConnector hubsMemoryFunctional organizationBrainModularity measureRecollectionConnectivity featuresEncodingCognitionNeuroanatomyLocal measurementsDifferences
2024
A spatially constrained independent component analysis jointly informed by structural and functional network connectivity
Fouladivanda M, Iraji A, Wu L, van Erp T, Belger A, Hawamdeh F, Pearlson G, Calhoun V. A spatially constrained independent component analysis jointly informed by structural and functional network connectivity. Network Neuroscience 2024, 8: 1212-1242. PMID: 39735500, PMCID: PMC11674407, DOI: 10.1162/netn_a_00398.Peer-Reviewed Original ResearchIntrinsic connectivity networksFunctional brain connectivityBrain connectivityStructural connectivityFunctional connectivityIndependent component analysisResting-state functional MRIAnalysis of group differencesBrain functional organizationFunctional network connectivityStructural-functional connectivityNeuroimaging studiesFunctional MRIWhole-brain tractographyGroup differencesRs-fMRIBrain disordersFunctional couplingSchizophreniaStatistical analysis of group differencesSubject levelFunctional organizationConnectivity networksBrainDiffusion-weighted MRIThe cell-type underpinnings of the human functional cortical connectome
Anderson K, Chopra S, Dhamala E, Emani P, Gerstein M, Margulies D, Holmes A. The cell-type underpinnings of the human functional cortical connectome. Nature Neuroscience 2024, 28: 150-160. PMID: 39572742, DOI: 10.1038/s41593-024-01812-2.Peer-Reviewed Original ResearchSingle-nucleus RNA sequencing dataCell-type distributionRNA sequencing dataMicroarray dataSingle-nucleusIn vivo organizationCortical sheetCortical connectomeAllen Human Brain AtlasCell typesFunctional magnetic resonance imagingCellular fingerprintsCortical tissue samplesHuman Brain AtlasOrganization of cortexFunctional organization of cortexCellular compositionBrain atlasesFunctional organizationCellsEnriched cellsAssociative territoryFunctional propertiesTissue samplesSpatial topography
2023
Brn3b regulates the formation of fear-related midbrain circuits and defensive responses to visual threat
Lee H, Weinberg-Wolf H, Lee H, Lee T, Conte J, Godoy-Parejo C, Demb J, Rudenko A, Kim IJ. Brn3b regulates the formation of fear-related midbrain circuits and defensive responses to visual threat. PLOS Biology 2023, 21: e3002386. PMID: 37983249, PMCID: PMC10695396, DOI: 10.1371/journal.pbio.3002386.Peer-Reviewed Original ResearchConceptsTranscription factor Brn3bLoss of neuronsVisual threatLateral posterior nucleusMutant mice displayDefensive responsesDefensive freezing responsesPosterior nucleusTachykinin 2Mice displayMidbrain circuitVisual circuitsNeural circuitryBrn3bSpecific genetic componentsFreezing responseFear-associated behaviorsSocial isolationTac2Behavioral phenotypesMolecular mechanismsFunctional organizationGenetic componentResponseSimilar mechanismDevelopmental differences in functional organization of multispectral networks
Petro N, Picci G, Embury C, Ott L, Penhale S, Rempe M, Johnson H, Willett M, Wang Y, Stephen J, Calhoun V, Doucet G, Wilson T. Developmental differences in functional organization of multispectral networks. Cerebral Cortex 2023, 33: 9175-9185. PMID: 37279931, PMCID: PMC10505424, DOI: 10.1093/cercor/bhad193.Peer-Reviewed Original ResearchConceptsSpontaneous cortical activityPhase coherenceImaginary partFunctional magnetic resonance imaging measuresConsistent with previous workFunctional brain organizationLimbic cortical regionsFunctional organizationBrain connectivityFunction of increasing ageEyes-closed restGamma bandSpectral specificityConnectivity matrixBrain regionsCanonical deltaBrain organizationBrain activityFunctional connectivityDevelopmental differencesBandCortical regionsCanonical networksCortical activityMagnetic resonance imaging measuresLinking resting-state network fluctuations with systems of coherent synaptic density: A multimodal fMRI and 11C-UCB-J PET study
Fang X, Volpi T, Holmes S, Esterlis I, Carson R, Worhunsky P. Linking resting-state network fluctuations with systems of coherent synaptic density: A multimodal fMRI and 11C-UCB-J PET study. Frontiers In Human Neuroscience 2023, 17: 1124254. PMID: 36908710, PMCID: PMC9995441, DOI: 10.3389/fnhum.2023.1124254.Peer-Reviewed Original ResearchSynaptic densityRSN activityResting-state network connectivityRSN functional connectivityAnterior default mode networkJ PET studyResting-state fMRIBrain functional organizationDefault mode networkHealthy adult participantsExecutive control networkRSN connectivityFunctional organizationPsychiatric disordersMedial prefrontalSalience networkPET studiesFunctional connectivityHealthy agingFractional amplitudeLow-frequency fluctuationsNeurophysiological linkSynaptic architectureAdult participantsDefault-mode activity
2022
Brain–phenotype models fail for individuals who defy sample stereotypes
Greene AS, Shen X, Noble S, Horien C, Hahn CA, Arora J, Tokoglu F, Spann MN, Carrión CI, Barron DS, Sanacora G, Srihari VH, Woods SW, Scheinost D, Constable RT. Brain–phenotype models fail for individuals who defy sample stereotypes. Nature 2022, 609: 109-118. PMID: 36002572, PMCID: PMC9433326, DOI: 10.1038/s41586-022-05118-w.Peer-Reviewed Original ResearchConceptsBrain-phenotype relationshipsBrain functional organizationCognitive constructsIndividual differencesNeurocognitive measuresBrain activityNeurocognitive scoresStereotypical profileNeural targetsClinical interventionsNeural circuitsFunctional organizationIndividualsSuch relationshipsData-driven approachRelationshipStereotypesLarge-scale differences in functional organization of left- and right-handed individuals using whole-brain, data-driven analysis of connectivity
Tejavibulya L, Peterson H, Greene A, Gao S, Rolison M, Noble S, Scheinost D. Large-scale differences in functional organization of left- and right-handed individuals using whole-brain, data-driven analysis of connectivity. NeuroImage 2022, 252: 119040. PMID: 35272202, PMCID: PMC9013515, DOI: 10.1016/j.neuroimage.2022.119040.Peer-Reviewed Original ResearchConceptsHanded individualsFunctional connectivityLanguage areasWhole-brain functional connectivityRight-handed individualsFunctional organizationWhole-brain levelIndividual differencesHandedness differencesHandedness effectsFunctional connectomeBrain levelsSomatosensory cortexNetworks of interestWhole brainSex differencesBrainConnectomeIndividualsData-driven analysisConnectivityDistinct patternsLateralizationDifferencesSimilar amounts
2021
A reachable probability approach for the analysis of spatio-temporal dynamics in the human functional network
Gao Q, Xiang Y, Zhang J, Luo N, Liang M, Gong L, Yu J, Cui Q, Sepulcre J, Chen H. A reachable probability approach for the analysis of spatio-temporal dynamics in the human functional network. NeuroImage 2021, 243: 118497. PMID: 34428571, DOI: 10.1016/j.neuroimage.2021.118497.Peer-Reviewed Original ResearchConceptsHuman brainBrain network systemsBrain functional systemsHierarchical functional organizationPrimary sensory cortexHuman functional networkMode networkMultisensory integration regionsPerceptual modalitiesMultisensory integrationSensory cortexNetwork systemAnalysis of spatio-temporal dynamicsFunctional networksTransition probabilitiesNeuronal circuitsDynamic architectureFunctional systemsFunctional organizationLocalize functional regionsDifferential patternConnectional organizationConnection structureProbability approachNetwork steady state
2020
Organization, Function, and Development of the Mouse Retinogeniculate Synapse
Liang L, Chen C. Organization, Function, and Development of the Mouse Retinogeniculate Synapse. Annual Review Of Vision Science 2020, 6: 261-285. PMID: 32936733, DOI: 10.1146/annurev-vision-121219-081753.Peer-Reviewed Original ResearchConceptsRetinogeniculate synapseDistinct retinal ganglion cell typesRetinal ganglion cell typesGanglion cell typesImage-forming pathwayVisual thalamusThalamocortical neuronsVisual pathwayExperimental modelCircuit organizationThalamusSynapseMiceCell typesFunctional organizationRecent studiesPowerful experimental modelCurrent understandingVisual spaceVisual experiencePathwayNeuronsRGCs
2019
Individualized functional networks reconfigure with cognitive state
Salehi M, Karbasi A, Barron DS, Scheinost D, Constable RT. Individualized functional networks reconfigure with cognitive state. NeuroImage 2019, 206: 116233. PMID: 31574322, PMCID: PMC7216521, DOI: 10.1016/j.neuroimage.2019.116233.Peer-Reviewed Original ResearchConceptsCognitive stateFunctional networksMultiple cognitive statesFunctional network organizationFunctional organizationBrain functional networksTask demandsFMRI dataSimilar tasksParcellation approachHuman brainNetwork organizationExtensive evidenceMultiple subjectsBrainNetwork membershipTaskOrganizationSubjectsParcellationSuch reconfigurationMeasuresMembershipFindingsSuch definitionsGradient Theories of Brain Activation: a Novel Application to Studying the Parental Brain
Rutherford HJV, Xu J, Worhunsky PD, Zhang R, Yip SW, Morie KP, Calhoun VD, Kim S, Strathearn L, Mayes LC, Potenza MN. Gradient Theories of Brain Activation: a Novel Application to Studying the Parental Brain. Current Behavioral Neuroscience Reports 2019, 6: 119-125. PMID: 32154064, PMCID: PMC7062306, DOI: 10.1007/s40473-019-00182-5.Peer-Reviewed Original ResearchDifferent sensory modalitiesParental brainNeural substratesSensory modalitiesBlood oxygenation level-dependent (BOLD) responseGeneral linear model-based analysisBrain functional organizationLevel-dependent responsesSad facesLinear model-based analysisBrain activationVisual cuesBrain researchInfant cryingFMRI datasetsFunctional networksSubcortical structuresFunctional organizationPreliminary findingsModel-based analysisIndependent component analysisCommon responseBrainCuesFaceOdor coding in the antenna of the tsetse fly Glossina morsitans
Soni N, Chahda JS, Carlson JR. Odor coding in the antenna of the tsetse fly Glossina morsitans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 14300-14308. PMID: 31221757, PMCID: PMC6628836, DOI: 10.1073/pnas.1907075116.Peer-Reviewed Original ResearchConceptsTsetse fly Glossina morsitansClasses of sensillaFruit flyPhysiological analysisAlarm pheromoneDifferent response dynamicsOlfactory sensillaFly antennaOlfactory cuesCellular basisWide diversityTsetse fliesSensillaFliesDifferent functionsDifferent odor stimuliGlossina morsitansPheromoneTsetseFunctional organizationHostDrosophilaMorphological typesOdorantsStriking differenceSocioeconomic status in children is associated with spontaneous activity in right superior temporal gyrus
Biazoli C, Salum G, Gadelha A, Rebello K, Moura L, Pan P, Brietzke E, Miguel E, Rohde L, Bressan R, Jackowski A, Sato J. Socioeconomic status in children is associated with spontaneous activity in right superior temporal gyrus. Brain Imaging And Behavior 2019, 14: 961-970. PMID: 30868400, DOI: 10.1007/s11682-019-00073-z.Peer-Reviewed Original ResearchConceptsRight superior temporal gyrusSuperior temporal gyrusTemporal gyrusExtended language networkDifferent developmental trajectoriesBrain functional organizationSchool-based sampleFunctional organizationStructural neuroimaging findingsCognitive controlSocioeconomic statusLanguage networkExternalizing problemsInternalizing problemsDevelopmental trajectoriesEmotional problemsSpontaneous activityRegional spontaneous activityLanguage processingFMRI featuresBrain regionsBrain areasNeuroimaging findingsFunctional networksLinguistic environment
2018
Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins
Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Proteomes 2018, 6: 48. PMID: 30487426, PMCID: PMC6313906, DOI: 10.3390/proteomes6040048.Peer-Reviewed Original ResearchProximity labelingLabel-free quantitation mass spectrometryReceptor-type tyrosine-protein phosphatase zetaProximity labeling approachCell-cell contactSynaptic cleftPost-synaptic specializationsProteomic contentSynapse heterogeneitySynCAM 1Confocal microcopySurface proteinsCell surfaceProteomeSuper-resolution imagingCultured cortical neuronsMammalian brainLabeling approachMolecular compositionReporterProteinCortical neuronsFunctional organizationExcitatory synapsesDiverse setTask-induced brain state manipulation improves prediction of individual traits
Greene AS, Gao S, Scheinost D, Constable RT. Task-induced brain state manipulation improves prediction of individual traits. Nature Communications 2018, 9: 2807. PMID: 30022026, PMCID: PMC6052101, DOI: 10.1038/s41467-018-04920-3.Peer-Reviewed Original ResearchConceptsBrain statesIndividual differencesBrain-behavior relationshipsFluid intelligence scoresTask-based functional connectivity analysisResting-state fMRI dataBrain functional organizationFunctional connectivity analysisCognitive tasksFluid intelligenceIntelligence scoresFunctional connectivityFMRI dataConnectivity analysisHuman behaviorIndividual traitsTaskCertain tasksFunctional organizationOutperform modelsSuch relationshipsCognitionState manipulationIntelligenceVariance
2017
The Laminar Organization of Piriform Cortex Follows a Selective Developmental and Migratory Program Established by Cell Lineage
Martin-Lopez E, Ishiguro K, Greer CA. The Laminar Organization of Piriform Cortex Follows a Selective Developmental and Migratory Program Established by Cell Lineage. Cerebral Cortex 2017, 29: 1-16. PMID: 29136113, PMCID: PMC7199997, DOI: 10.1093/cercor/bhx291.Peer-Reviewed Original ResearchConceptsLaminar specificityLaminar organizationNeurogenesis/gliogenesisPrimary afferent inputNeurogenic patternPiriform cortexAfferent inputNeurogenic gradientOlfactory bulbLayers IIGlial organizationNeuronal migrationPC progenitorsLaminar developmentCortexFunctional organizationClonal analysisCell lineagesLikely roleEarly developmentPaleocortexAnteriorNeurogenesisSpecificityGliogenesisFunctional Connectivity Parcellation of the Human Thalamus by Independent Component Analysis
Zhang S, Li CR. Functional Connectivity Parcellation of the Human Thalamus by Independent Component Analysis. Brain Connectivity 2017, 7: 602-616. PMID: 28954523, PMCID: PMC5695755, DOI: 10.1089/brain.2017.0500.Peer-Reviewed Original ResearchConceptsWhole-brain connectivityThalamic connectivityFunctional connectivityState functional magnetic resonanceTime coursePrimary motor cortexWhole-brain functional connectivitySeed region analysisBrain functional connectivityFunctional magnetic resonanceIndependent component time coursesMotor cortexThalamic subdivisionsHuman thalamusCaudate nucleusThalamic clustersThalamusSubcortical regionsBrain regionsRegional functionPatterns of connectivityAffective functionsFunctional organizationMagnetic resonanceFunctional clustersConnectome-based Models Predict Separable Components of Attention in Novel Individuals
Rosenberg MD, Hsu WT, Scheinost D, Constable R, Chun MM. Connectome-based Models Predict Separable Components of Attention in Novel Individuals. Journal Of Cognitive Neuroscience 2017, 30: 160-173. PMID: 29040013, DOI: 10.1162/jocn_a_01197.Peer-Reviewed Original ResearchConceptsConnectome-based predictive modelingAttention Network TaskExecutive controlIntrinsic functional organizationRT variabilityANT performanceInfluential modelFunctional connectivityBrain's intrinsic functional organizationComponents of attentionExecutive control scoresResting-state functional connectivityResting-state dataFunctional brain networksFunctional organizationTask-based dataAttentional abilitiesUpcoming stimulusExplicit taskSustained attentionFMRI scanningAttention factorNovel individualsAdditional independent componentNetwork tasks
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