Notebook Artifact Registry

Computational analysis artifacts linked to analyses and knowledge graph entities

Filter by tag:All APOE4 Aging Allen Institute Alzheimer's CRISPR Circuit Analysis Cross-Age Analysis Epigenetics Gene Expression Immune Response Microglia Mouse Model Neural Dynamics Neurodegeneration Neuroinflammation Protein Propagation SEA-AD Senescent Cells Senolytics Structural Biology Tau Therapeutics []aging allen-brain allen-brain-atlas allen-institute alzheimers analysis artifact astrocytes auto biomarkers cell-atlas cell-types ci demo draft epigenetics forge-tools gene-editing gene-expression go hypotheses hypothesis-analysis kegg knowledge-gap lipid-rafts microglia neurodegeneration neuroinflammation neurons notebook pathway-enrichment reactome scanpy sea-ad seeded senescence showcase single-cell statistics stub tau template test transcriptomics tsne umap walkthrough

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Gene Expression Changes in Aging Mouse Brain Predicting Neurodegenerative Vulnerability

Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for aging mouse brain transcriptomics.

showcase forge-tools transcriptomics neurodegeneration

📊 Gene expression changes in aging mouse brain predicting neurodegenerative vulnerability

Created: 2026-04-16

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Neuroinflammation and Microglial Priming in Early Alzheimer's Disease

Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for microglial priming in early AD.

showcase forge-tools neuroinflammation neurodegeneration

📊 Neuroinflammation and microglial priming in early Alzheimer's Disease

Created: 2026-04-16

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CRISPR-Based Therapeutic Approaches for Neurodegenerative Diseases

Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for CRISPR neurodegeneration therapy research.

showcase forge-tools gene-editing neurodegeneration

📊 CRISPR-based therapeutic approaches for neurodegenerative diseases

Created: 2026-04-16

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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: 2026-04-13

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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: 2026-04-13

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All Notebooks (2) (filtered by: allen-brain)

Allen Brain Atlas Analysis Template

General-purpose template for analyzing gene expression data from the Allen Brain Atlas. Includes AllenSDK integration, gene expression queries, differential expression analysis, and Enrichr pathway en

allen-brain-atlas gene-expression template neurodegeneration demo

MAPT APP APOE SNCA PSEN1

Created: 2026-04-23

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SEA-AD Allen Brain Cell Atlas — Cell-Type Vulnerability Analysis

Comprehensive analysis of the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) dataset. Differential expression analysis across 7 major cell types, heatmaps of AD-associated genes (TREM2, APOE,

sea-ad allen-brain cell-atlas neurodegeneration demo

📊 Which specific cell types show greatest vulnerability in AD based on SEA-AD transcriptomic analysis? (neurodegeneration)

Created: 2026-04-23

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