Notebook Artifact Registry

Computational analysis artifacts linked to analyses and knowledge graph entities

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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

[]

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 (11) (filtered by: draft)

What are the optimal timing windows for TREM2 agonism vs antagonism across disease progression stages? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-11-gap-debate-20260410-112636-141592ba. The debate highlighted that TREM2 therapeutic targeting remains contested across disease stages, but no clea

draft auto ci

📊 What are the optimal timing windows for TREM2 agonism vs antagonism across disease progression stages? (neurodegeneration)

Created: 2026-04-12

How can CRISPR systems achieve persistent therapeutic effects while avoiding chronic immune responses to Cas proteins in the CNS? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-11-gap-debate-20260410-112625-c44578b5. The debate highlighted that long-term CRISPR expression triggers immune responses, but epigenetic therapies

draft auto ci

📊 How can CRISPR systems achieve persistent therapeutic effects while avoiding chronic immune responses to Cas proteins in the CNS? (gene therapy)

Created: 2026-04-12

Can P16INK4A expression reliably distinguish harmful from beneficial senescent microglia in neurodegeneration? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-11-gap-debate-20260410-112619-9c3c13d2. The debate proposed P16INK4A-guided targeting but the Skeptic noted microglia exist in complex activation st

draft auto ci

📊 Can P16INK4A expression reliably distinguish harmful from beneficial senescent microglia in neurodegeneration? (neurodegeneration)

Created: 2026-04-12

Which neural cell types exhibit the most pronounced gene expression alterations in neurodegeneration? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-11-gap-debate-20260410-112336-ccdef571. The debate generated therapeutic hypotheses targeting different cell types but never resolved the fundamenta

draft auto ci

📊 Which neural cell types exhibit the most pronounced gene expression alterations in neurodegeneration? (neurodegeneration)

Created: 2026-04-11

Does SYK activation provide neuroprotection or exacerbate neuroinflammation in established Alzheimer's disease? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-11-gap-debate-20260410-111113-052488a8. The debate revealed fundamental uncertainty about whether enhancing TYROBP-SYK signaling would be beneficial

draft auto ci

📊 Does SYK activation provide neuroprotection or exacerbate neuroinflammation in established Alzheimer's disease? (neurodegeneration)

Created: 2026-04-11

How do disease-associated mutations in G3BP1 or its binding partners alter stress granule dynamics? — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-06-gap-pubmed-20260406-041428-e14e6524. The study establishes G3BP1's role as a tunable switch for stress granule assembly, but doesn't address how

draft auto ci

📊 How do disease-associated mutations in G3BP1 or its binding partners alter stress granule dynamics? (neurodegeneration)

Created: 2026-04-06

Unable to extract research questions - transcript appears to be empty — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-04-gap-debate-20260403-222510-20260402. The provided transcript contains only speaker labels [Theorist] and [Synthesizer] with no actual debate cont

draft auto ci

📊 Unable to extract research questions - transcript appears to be empty (methodology)

Created: 2026-04-06

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What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's disease pathogenesis through the gut-brain axis? — Analysis Notebook

Computational analysis notebook for 'What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's disease pathogenesis through the gut-brain axis?'. Domain: neurodegeneration. Rese

draft artifact notebook

📊 What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's disease pathogenesis through the gut-brain axis? (neurodegeneration)

Created: 2026-04-04

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APOE4-driven lipid metabolism dysregulation in astrocytes and its role in AD — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-04-gap-apoe4-lipid-metabolism. APOE4 is the strongest genetic risk factor for late-onset AD. How APOE4 specifically disrupts lipid homeostasis in as

draft auto ci

📊 APOE4-driven lipid metabolism dysregulation in astrocytes and its role in AD (neuroscience)

Created: 2026-04-04

epigenetic reprogramming aging neurons — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-04-gap-20260404-060512. epigenetic reprogramming aging neurons

draft auto ci

📊 epigenetic reprogramming aging neurons (neurodegeneration)

Created: 2026-04-04

Investigate prion-like spreading of tau pathology through connected brain regions — Analysis Notebook

CI-generated notebook stub for analysis SDA-2026-04-04-gap-20260404-052358. Investigate prion-like spreading of tau pathology through connected brain regions

draft auto ci

📊 Investigate prion-like spreading of tau pathology through connected brain regions (neurodegeneration)

Created: 2026-04-04