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 (7) (filtered by: Epigenetics)

Epigenetic reprogramming in aging neurons

SciDEX Analysis | ID: SDA-2026-04-02-gap-epigenetic-reprog-b685190e

epigenetics neurodegeneration statistics
Created: 2026-04-02
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CRISPR-Based Therapeutic Approaches for Neurodegenerative Diseases

Analysis ID: SDA-2026-04-02-gap-crispr-neurodegeneration-20260402 Date: 2026-04-02 Domain: neurodegeneration Hypotheses Generated: 5 Knowledge Graph Edges: 15

CRISPR SEA-AD epigenetics gene-expression hypothesis-analysis
📊 CRISPR-based therapeutic approaches for neurodegenerative diseases (neurodegeneration)
Created: 2026-04-02
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Epigenetic Reprogramming in Aging Neurons — Mechanistic Analysis

Investigate mechanisms of epigenetic reprogramming in aging neurons. How do changes in DNA methylation, histone modification, and chromatin remodeling contribute to neurodegeneration risk?

SEA-AD epigenetics gene-expression hypothesis-analysis microglia
📊 Epigenetic reprogramming in aging neurons (neurodegeneration)
Created: 2026-04-02
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Epigenetic reprogramming in aging neurons - Rich Analysis Notebook

Executed notebook with gene expression plots, pathway enrichment, radar charts, and statistical tests for: Investigate mechanisms of epigenetic reprogramming in aging neurons...

Aging Epigenetics Gene Expression Neurodegeneration
📊 Epigenetic reprogramming in aging neurons (neurodegeneration)
Created: 2026-04-02
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Astrocyte reactivity subtypes in neurodegeneration

What are the mechanisms underlying astrocyte reactivity subtypes in neurodegeneration?

epigenetics gene-expression neurodegeneration statistics
📊 Astrocyte reactivity subtypes in neurodegeneration (neurodegeneration)
Created: 2026-04-01
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Epigenetic clocks and biological aging in neurodegeneration

What are the mechanisms underlying epigenetic clocks and biological aging in neurodegeneration?

epigenetics gene-expression neurodegeneration statistics
📊 Epigenetic clocks and biological aging in neurodegeneration (neurodegeneration)
Created: 2026-04-01
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Astrocyte reactivity subtypes in neurodegeneration

Analysis ID: SDA-2026-04-01-gap-007 Date: 2026-04-02 Domain: neurodegeneration Hypotheses Generated: 7 Knowledge Graph Edges: 20

SEA-AD epigenetics gene-expression hypothesis-analysis microglia
📊 Astrocyte reactivity subtypes in neurodegeneration (neurodegeneration)
Created: 2026-04-01
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