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

[]
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

[]
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 (6) (filtered by: Neuroinflammation)

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 citations.

showcase forge-tools neuroinflammation neurodegeneration
📊 Neuroinflammation and microglial priming in early Alzheimer's Disease (neurodegeneration)
Created: 2026-04-11
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Immune Atlas: Neuroinflammation in Neurodegeneration

Analysis ID: SDA-2026-04-02-gap-immune-atlas-neuroinflam-20260402 Date: 2026-04-02 Domain: Neuroinflammation

gene-expression microglia neurodegeneration neuroinflammation statistics
📊 Immune atlas neuroinflammation analysis in neurodegeneration (Neuroinflammation)
Created: 2026-04-02
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Neuroinflammation resolution mechanisms and pro-resolving mediators - Rich Analysis Notebook

Enhanced notebook with gene expression, pathway enrichment, and statistical analysis for: What are the mechanisms underlying neuroinflammation resolution mechanisms and pro-resolving mediato

Neuroinflammation Immune Response Therapeutics
📊 Neuroinflammation resolution mechanisms and pro-resolving mediators (neurodegeneration)
Created: 2026-04-02
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Microglia-astrocyte crosstalk amplification loops in neurodegeneration — Gene Expression & Pathway Analysis

Analysis ID: SDA-2026-04-01-gap-009 Date: 2026-04-03 Focus: glial crosstalk amplification loops in neuroinflammation

gene-expression microglia neurodegeneration neuroinflammation statistics
📊 Microglia-astrocyte crosstalk amplification loops in neurodegeneration (neurodegeneration)
Created: 2026-04-01
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Microglia-astrocyte crosstalk amplification loops in neurodegeneration — Statistical Deep Dive

Analysis ID: SDA-2026-04-01-gap-009 Date: 2026-04-03

gene-expression microglia neurodegeneration neuroinflammation statistics
📊 Microglia-astrocyte crosstalk amplification loops in neurodegeneration (neurodegeneration)
Created: 2026-04-01
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Neuroinflammation Resolution Mechanisms and Pro-Resolving Mediators

How do specialized pro-resolving mediators (SPMs) resolve neuroinflammation, and can their pathways be therapeutically enhanced?

gene-expression microglia neurodegeneration neuroinflammation senescence
📊 Neuroinflammation resolution mechanisms and pro-resolving mediators (neurodegeneration)
Created: 2026-04-01
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