Notebook Artifact Registry

Computational analysis artifacts linked to analyses and knowledge graph entities

AllAPOE4AgingAllen InstituteAlzheimer'sCRISPRCircuit AnalysisCross-Age AnalysisEpigeneticsGene ExpressionImmune ResponseMicrogliaMouse ModelNeural DynamicsNeurodegenerationNeuroinflammationProtein PropagationSEA-ADSenescent CellsSenolyticsStructural BiologyTauTherapeutics[]agingalzheimersanalysisartifactastrocytesautobiomarkerscell-typescidraftepigeneticsforge-toolsgene-editinggene-expressionhypothesis-analysisknowledge-gaplipid-raftsmicroglianeurodegenerationneuroinflammationneuronsnotebooksea-adsenescenceshowcasesingle-cellstatisticsstubtautranscriptomicswalkthrough

🌟 Spotlight Notebooks

Mitochondrial Dysfunction as a Driver of Neurodegeneration

How does mitochondrial dysfunction drive neurodegeneration across AD, PD, and ALS? Characterize PINK1/Parkin mitophagy pathway, mtDNA damage, ETC complex activity, and ROS generati

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Created: 2026-04-12
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Tau Pathology Propagation in Tauopathies — Mechanistic Dissection

How does misfolded tau spread through the brain in tauopathies? Characterize prion-like propagation mechanisms, cell-to-cell transfer, and the role of MAPT mutations, ApoE genotype

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Created: 2026-04-12
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Neuroinflammation and microglial priming in early Alzheimer's Disease — Analysis Notebook

Mechanistic links between early microglial priming states, neuroinflammatory signaling, and AD progression. Forge-powered analysis with 14 hypotheses, 105 KG edges, and PubMed cita

showcase forge-tools neuroinflammation neurodegeneration
📊 Neuroinflammation and microglial priming in early Alzheimer's Disease
Created: 2026-04-11
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Gene expression changes in aging mouse brain predicting neurodegenerative vulnerability — Analysis Notebook

Forge-powered analysis: 28 hypotheses, 216 KG edges, PubMed + STRING + Open Targets + ClinVar. 10 code cells, 5 plots.

showcase forge-tools transcriptomics neurodegeneration
📊 Gene expression changes in aging mouse brain predicting neurodegenerative vulnerability
Created: 2026-04-11
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CRISPR-based therapeutic approaches for neurodegenerative diseases — Analysis Notebook

CRISPR-based therapeutic approaches for neurodegenerative diseases (Alzheimer, Parkinson, Huntington). Forge-powered analysis with 14 hypotheses, 431 KG edges, and PubMed citations

showcase forge-tools gene-editing neurodegeneration
📊 CRISPR-based therapeutic approaches for neurodegenerative diseases
Created: 2026-04-11
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All Notebooks (1) (filtered by: Circuit Analysis)

Circuit-Level Neural Dynamics in Neurodegeneration

Analyze circuit-level changes in neurodegeneration using Allen Institute Neural Dynamics data. Focus on how ion channel dysfunction and synaptic failure drive progressive circuit collapse in AD, PD, a

Allen Institute Neural Dynamics Circuit Analysis Neurodegeneration
📊 Circuit-level neural dynamics in neurodegeneration (neuroscience)
Created: 2026-04-02
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