Notebook Artifact Registry
Computational analysis artifacts linked to analyses and knowledge graph entities
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🌟 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
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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
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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
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
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
Created: 2026-04-11
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All Notebooks (70) (filtered by: gene-expression)
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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Proteostasis Enhancement via APOE Chaperone Targeting
Hypothesis ID: h-5d943bfc | Composite Score: 0.74/1.00
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-04
APOE-Dependent Autophagy Restoration
Hypothesis ID: h-51e7234f | Composite Score: 0.80/1.00
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-04
Targeted Butyrate Supplementation for Microglial Phenotype Modulation
Hypothesis ID: h-3d545f4e | Composite Score: 0.79/1.00
gene-expression hypothesis-analysis microglia neurodegeneration statistics
Created: 2026-04-04
Gamma entrainment therapy to restore hippocampal-cortical synchrony
Hypothesis ID: h-bdbd2120
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-04
Aging Mouse Brain Atlas: Cross-Age Gene Expression Analysis
Identify age-related gene expression changes across hippocampus, cortex, and cerebellum to understand aging-neurodegeneration overlap
aging gene-expression neurodegeneration statistics
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
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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
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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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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Tau propagation mechanisms and therapeutic interception points
Analysis ID: SDA-2026-04-02-gap-tau-prop-20260402003221
gene-expression microglia neurodegeneration statistics tau
Created: 2026-04-02
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Circuit-level neural dynamics in neurodegeneration
Analyze circuit-level changes in neurodegeneration using Allen Institute Neural Dynamics data. Focus on: (1) hippocampal circuit disruption, (2) cortical dynamics alterations, (3) sensory processing c
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-02
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Gene Expression in Aging Mouse Brain Predicting Neurodegeneration (v1)
What gene expression changes in the aging mouse brain predict neurodegenerative vulnerability? Using Allen Brain Atlas aging datasets, identify conserved transcriptomic signatures across 3, 12, 18, an
aging gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-02
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Cellular Senescence Signatures in Aging Mouse Brain (v5)
Which cellular senescence markers in aging mouse brain best predict downstream neurodegeneration risk? Focus on p21/p16 axis, SASP factors, and their interaction with neuroinflammatory cascades.
aging gene-expression hypothesis-analysis microglia neurodegeneration
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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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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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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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 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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TDP-43 phase separation therapeutics for ALS-FTD — Gene Expression & Pathway Analysis
Analysis ID: SDA-2026-04-01-gap-006
Date: 2026-04-03
Focus: phase separation dynamics and RNA-protein granule pathology
gene-expression neurodegeneration statistics
Created: 2026-04-01
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TDP-43 phase separation therapeutics for ALS-FTD — Statistical Deep Dive
Analysis ID: SDA-2026-04-01-gap-006
Date: 2026-04-03
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Astrocyte reactivity subtypes in neurodegeneration
What are the mechanisms underlying astrocyte reactivity subtypes in neurodegeneration?
epigenetics gene-expression neurodegeneration statistics
Created: 2026-04-01
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Blood-brain barrier transport mechanisms for antibody therapeutics
What are the mechanisms underlying blood-brain barrier transport mechanisms for antibody therapeutics?
gene-expression neurodegeneration statistics
Created: 2026-04-01
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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
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
Created: 2026-04-01
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Microglia-astrocyte crosstalk amplification loops in neurodegeneration
What are the mechanisms underlying microglia-astrocyte crosstalk amplification loops in neurodegeneration?
gene-expression microglia neurodegeneration statistics
Created: 2026-04-01
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APOE4 Structural Biology and Therapeutic Targeting Strategies
What are the structural mechanisms underlying APOE4 pathogenicity and how can they be exploited for therapeutic intervention?
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Autophagy-lysosome pathway convergence across neurodegenerative diseases — Gene Expression & Pathway Analysis
Analysis ID: SDA-2026-04-01-gap-011
Date: 2026-04-03
Focus: autophagy-lysosome convergence across neurodegenerative diseases
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Autophagy-lysosome pathway convergence across neurodegenerative diseases — Statistical Deep Dive
Analysis ID: SDA-2026-04-01-gap-011
Date: 2026-04-03
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Autophagy-lysosome pathway convergence across neurodegenerative diseases
What are the mechanisms underlying autophagy-lysosome pathway convergence across neurodegenerative diseases?
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Digital biomarkers and AI-driven early detection of neurodegeneration
What are the mechanisms underlying digital biomarkers and ai-driven early detection of neurodegeneration?
biomarkers gene-expression neurodegeneration statistics
Created: 2026-04-01
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Senolytic therapy for age-related neurodegeneration
What are the mechanisms underlying senolytic therapy for age-related neurodegeneration?
gene-expression neurodegeneration senescence statistics
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
Created: 2026-04-01
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Gut Microbiome Dysbiosis and Parkinson's Disease via the Gut-Brain Axis
Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for gut-brain axis / Parkinson's disease research.
showcase forge-tools gene-expression neurodegeneration
Created: 2026-04-01
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What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's disease pathogenesis through the gut-brain axis?
What are the mechanisms underlying what are the mechanisms by which gut microbiome dysbiosis influences parkinson's disease pathogenesis through the gut-brain axis??
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Mitochondrial transfer between neurons and glia
Analysis ID: SDA-2026-04-01-gap-20260401231108
gene-expression microglia neurodegeneration statistics
Created: 2026-04-01
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Protein aggregation cross-seeding across neurodegenerative diseases
What are the mechanisms underlying protein aggregation cross-seeding across neurodegenerative diseases?
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Sleep disruption as cause and consequence of neurodegeneration — Gene Expression & Pathway Analysis
Analysis ID: SDA-2026-04-01-gap-v2-18cf98ca
Date: 2026-04-03
Focus: bidirectional relationship between sleep disruption and neurodegeneration
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Sleep disruption as cause and consequence of neurodegeneration — Statistical Deep Dive
Analysis ID: SDA-2026-04-01-gap-v2-18cf98ca
Date: 2026-04-03
gene-expression microglia neurodegeneration statistics tau
Created: 2026-04-01
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Sleep Disruption as Cause and Consequence of Neurodegeneration
How do sleep disruptions both drive and result from neurodegenerative disease processes, and what therapeutic opportunities exist in this bidirectional relationship?
gene-expression microglia neurodegeneration statistics tau
Created: 2026-04-01
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RNA binding protein dysregulation across ALS FTD and AD
Analysis ID: SDA-2026-04-01-gap-v2-68d9c9c1
gene-expression neurodegeneration statistics
Created: 2026-04-01
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Synaptic pruning by microglia in early AD — Gene Expression & Pathway Analysis
Analysis ID: SDA-2026-04-01-gap-v2-691b42f1
Date: 2026-04-03
Focus: complement-mediated synaptic elimination in early Alzheimer pathology
gene-expression microglia neurodegeneration statistics
Created: 2026-04-01
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Synaptic pruning by microglia in early AD — Statistical Deep Dive
Analysis ID: SDA-2026-04-01-gap-v2-691b42f1
Date: 2026-04-03
gene-expression microglia neurodegeneration statistics
Created: 2026-04-01
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Synaptic pruning by microglia in early AD
Analysis ID: SDA-2026-04-01-gap-v2-691b42f1
gene-expression microglia neurodegeneration statistics
Created: 2026-04-01
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Mitochondrial transfer between astrocytes and neurons
Analysis ID: SDA-2026-04-01-gap-v2-89432b95
gene-expression 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
Created: 2026-04-01
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Perivascular Spaces and Glymphatic Clearance Failure in AD
How do perivascular space dysfunction and glymphatic clearance failure contribute to Alzheimer's disease pathogenesis?
gene-expression neurodegeneration statistics
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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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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TDP-43 phase separation therapeutics for ALS-FTD
What are the mechanisms underlying tdp-43 phase separation therapeutics for als-ftd?
gene-expression hypothesis-analysis neurodegeneration statistics
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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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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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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Autophagy-lysosome pathway convergence across neurodegenerative diseases
What are the mechanisms underlying autophagy-lysosome pathway convergence across neurodegenerative diseases?
gene-expression hypothesis-analysis neurodegeneration statistics
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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What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's disease pathogenesis through the gut-brain axis?
What are the mechanisms underlying what are the mechanisms by which gut microbiome dysbiosis influences parkinson's disease pathogenesis through the gut-brain axis??
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-01
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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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Mechanistic role of APOE in neurodegeneration
What are the mechanisms underlying mechanistic role of apoe in neurodegeneration?
gene-expression hypothesis-analysis lipid-rafts neurodegeneration statistics
Created: 2026-04-01
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Lipid raft composition changes in synaptic neurodegeneration
Investigate how lipid raft composition (cholesterol metabolism, sphingolipids) changes in synaptic membranes during neurodegeneration and their mechanistic role in amyloid-beta processing and synapse
gene-expression hypothesis-analysis lipid-rafts neurodegeneration statistics
Created: 2026-04-01
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Sleep disruption as cause and consequence of neurodegeneration
What are the mechanisms underlying sleep disruption as cause and consequence of neurodegeneration?
gene-expression hypothesis-analysis microglia neurodegeneration statistics
Created: 2026-04-01
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RNA binding protein dysregulation across ALS FTD and AD
What are the mechanisms underlying rna binding protein dysregulation across als ftd and ad?
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-01
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Synaptic pruning by microglia in early AD
What are the mechanisms underlying synaptic pruning by microglia in early ad?
gene-expression hypothesis-analysis microglia neurodegeneration statistics
Created: 2026-04-01
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Perivascular spaces and glymphatic clearance failure in AD
What are the mechanisms underlying perivascular spaces and glymphatic clearance failure in ad?
gene-expression hypothesis-analysis neurodegeneration statistics
Created: 2026-04-01
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