Notebook Artifact Registry
Computational analysis artifacts linked to analyses and knowledge graph entities
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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
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
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
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
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Created: 2026-04-13
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All Notebooks (24) (filtered by: SEA-AD)
ACSL4-Driven Ferroptotic Priming in Disease-Associated Microglia
Hypothesis ID: h-seaad-v4-26ba859b | Composite Score: 0.82/1.00
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-04
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Cell-Type Specific TREM2 Upregulation in DAM Microglia
Hypothesis ID: h-seaad-51323624 | Composite Score: 0.73/1.00
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-04
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SEA-AD Gene Expression Analysis: Microglia vs Neurons in Alzheimer's Disease
Notebook ID: SEA-AD-gene-expression-analysis
SEA-AD gene-expression microglia neurodegeneration statistics
Created: 2026-04-04
SEA-AD Gene Expression Analysis: Microglia vs Neurons
Differential gene expression analysis of Alzheimer's disease-related genes comparing microglia and neurons using Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) data. Includes heatmap, volcano p
SEA-AD Allen Institute Alzheimer's Gene Expression Microglia
APP APOE MAPT TREM2 CD33
Created: 2026-04-02
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Senescent Cell Clearance as Neurodegeneration Therapy
Analysis ID: SDA-2026-04-02-gap-senescent-clearance-neuro
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 5
Knowledge Graph Edges: 15
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-02
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Tau propagation mechanisms and therapeutic interception points
Analysis ID: SDA-2026-04-02-gap-tau-prop-20260402003221
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 77
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-02
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Metabolic reprogramming in neurodegenerative disease
Analysis ID: SDA-2026-04-02-gap-v2-5d0e3052
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 3
Knowledge Graph Edges: 31
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-02
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SEA-AD v4: Inhibitory Neuron Subtypes and Circuit Vulnerability in AD
Which inhibitory neuron subtypes show earliest transcriptomic divergence in AD? Characterize Sst, Pvalb, and Vip+ interneuron vulnerability and link to circuit dysfunction biomarkers.
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-02
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Cell-Type Vulnerability in Alzheimer's Disease — SEA-AD Transcriptomics (v3)
What cell types are most vulnerable in Alzheimer's Disease based on SEA-AD transcriptomic data? Identify differential gene expression, vulnerability scores, and regulatory networks in excitatory neuro
SEA-AD gene-expression microglia neurodegeneration statistics
Created: 2026-04-02
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Extracellular Vesicle Biomarkers for Early Alzheimer's Disease Detection
Which extracellular vesicle (EV) cargo proteins best discriminate early AD from controls? Characterize EV proteome from plasma, CSF, and brain tissue across disease stages using multi-cohort data.
SEA-AD biomarkers gene-expression hypothesis-analysis microglia
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
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
Created: 2026-04-02
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Cell-Type Vulnerability in Alzheimer's Disease — SEA-AD Transcriptomics (v4)
Extended SEA-AD analysis: identify cell-type-specific gene regulatory networks that predict vulnerability. Focus on super-enhancer-linked genes, TF binding, and cross-cell-type communication in AD-aff
SEA-AD gene-expression microglia neurodegeneration statistics
Created: 2026-04-02
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SEA-AD Gene Expression Profiling — Allen Brain Cell Atlas
Analysis ID: analysis-SEAAD-20260402
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 5
Knowledge Graph Edges: 63
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-02
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Mitochondrial transfer between neurons and glia
Analysis ID: SDA-2026-04-01-gap-20260401231108
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 0
SEA-AD gene-expression hypothesis-analysis microglia 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
Created: 2026-04-01
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APOE4 structural biology and therapeutic targeting strategies
Analysis ID: SDA-2026-04-01-gap-010
Date: 2026-04-01
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 81
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-01
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Selective vulnerability of entorhinal cortex layer II neurons in AD
Analysis ID: SDA-2026-04-01-gap-004
Date: 2026-04-01
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 83
SEA-AD gene-expression hypothesis-analysis knowledge-gap microglia
Created: 2026-04-01
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4R-tau strain-specific spreading patterns in PSP vs CBD
Analysis ID: SDA-2026-04-01-gap-005
Date: 2026-04-01
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 112
SEA-AD gene-expression hypothesis-analysis knowledge-gap microglia
Created: 2026-04-01
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Blood-brain barrier transport mechanisms for antibody therapeutics
Analysis ID: SDA-2026-04-01-gap-008
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 20
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-01
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Microglia-astrocyte crosstalk amplification loops in neurodegeneration
Analysis ID: SDA-2026-04-01-gap-009
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 20
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-01
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Digital biomarkers and AI-driven early detection of neurodegeneration
Analysis ID: SDA-2026-04-01-gap-012
Date: 2026-04-02
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 20
SEA-AD biomarkers gene-expression hypothesis-analysis microglia
Created: 2026-04-01
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Senolytic therapy for age-related neurodegeneration
Analysis ID: SDA-2026-04-01-gap-013
Date: 2026-04-01
Domain: neurodegeneration
Hypotheses Generated: 7
Knowledge Graph Edges: 282
SEA-AD gene-expression hypothesis-analysis microglia neurodegeneration
Created: 2026-04-01
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TREM2 agonism vs antagonism in DAM microglia
Analysis ID: SDA-2026-04-01-gap-001
Date: 2026-04-01
Domain: neurodegeneration
Key Hypotheses:
- TREM2-Dependent Microglial Senescence Transition (score: 0.705)
- Cell-Type Specific TREM
SEA-AD gene-expression hypothesis-analysis knowledge-gap microglia
Created: 2026-04-01
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