Computational analysis artifacts linked to analyses and knowledge graph entities
Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for aging mouse brain transcriptomics.
Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for microglial priming in early AD.
Real Forge-powered analysis: PubMed search, STRING PPI, Reactome pathways, gene annotations for CRISPR neurodegeneration therapy research.
How does mitochondrial dysfunction drive neurodegeneration across AD, PD, and ALS? Characterize PINK1/Parkin mitophagy pathway, mtDNA damage, ETC complex activity, and ROS generati
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
CI-generated notebook stub for analysis SDA-2026-04-21-gap-debate-20260417-033037-c43d12c2. The fundamental premise remains unvalidated despite extensive mechanistic speculation. Independent validatio
CI-generated notebook stub for analysis SDA-2026-04-10-gap-20260410-091440. Investigate mechanisms of epigenetic reprogramming in aging neurons, including DNA methylation changes, histone modification
CI-generated notebook stub for analysis SDA-2026-04-10-gap-20260410-091107. Investigate mechanisms of epigenetic reprogramming in aging neurons [TARGET_ARTIFACT type=analysis id=SDA-2026-04-04-gap-ep
CI-generated notebook stub for analysis SDA-2026-04-10-gap-20260410-090500. Investigate mechanisms of epigenetic reprogramming in aging neurons
CI-generated notebook stub for analysis SDA-NEUROINFLAM-BIOMARKERPANEL-0b9129bc. What is the optimal blood-based biomarker panel combining established markers (GFAP, p-tau217, NfL) and novel inflammat
CI-generated notebook stub for analysis SDA-2026-04-18-gap-debate-20260417-032952-48bdcbea. The debate highlighted compelling correlative evidence for ferroptosis markers in ALS tissues, but causality
CI-generated notebook stub for analysis SDA-BIOMNI-MICROBIO-337ee37a. How does the gut microbiome composition differ between PD patients and healthy controls, and which microbial metabolites correlate
CI-generated notebook stub for analysis SDA-2026-04-13-gap-debate-20260412-094612-a2e3bd09. The debate highlighted promising PTMs like K280 acetylation and O-GlcNAcylation but didn't resolve which mod
CI-generated notebook stub for analysis SDA-2026-04-14-gap-pubmed-20260410-174607-708e8d91. The finding that Mertk/Axl deficiency increases viral susceptibility contradicts the established paradigm th
CI-generated notebook stub for analysis SDA-BIOMNI-VARIANT_-b5b8e32f. Which non-coding variants at AD GWAS loci have functional evidence for gene regulation in brain cell types, and can we prioritize
CI-generated notebook stub for analysis SDA-BIOMNI-CAS13_PR-d6f415f0. Can optimized Cas13 guide RNAs selectively silence pathogenic MAPT splice variants (4R-tau) while preserving normal 3R-tau express
CI-generated notebook stub for analysis SDA-2026-04-04-SDA-2026-04-04-gap-debate-20260403-222618-c698b06a. Which metabolic biomarkers can distinguish therapeutic response from disease progression in n
CI-generated notebook stub for analysis SDA-BIOMNI-CLINICAL-b7a71edd. What is the current clinical trial landscape for AD therapeutics, and which mechanistic categories are over- vs under-represented
CI-generated notebook stub for analysis SDA-BIOMNI-CELL_CEL-a7eed9c5. Which ligand-receptor interactions between glial and neuronal populations are disrupted in AD, and do these disrupted communicatio
CI-generated notebook stub for analysis SDA-BIOMNI-GENE_REG-785b71fe. Which transcription factors drive the gene regulatory networks that distinguish vulnerable from resilient neuronal populations in
CI-generated notebook stub for analysis SDA-BIOMNI-SCRNA_AN-248caecc. Can standardized scRNA-seq processing and automated annotation identify novel cell states associated with AD pathology across mult
CI-generated notebook stub for analysis SDA-2026-04-13-gap-pubmed-20260410-143119-8ae42941. The abstract describes a novel mechanism where PIKFYVE inhibition triggers exocytosis of aggregation-prone p
CI-generated notebook stub for analysis SDA-2026-04-16-gap-pubmed-20260410-180503-a7a03974. The abstract suggests that Aβ-tau synergy could explain negative results from anti-Aβ trials, contradicting
CI-generated notebook stub for analysis SDA-2026-04-16-gap-pubmed-20260410-095709-4e97c09e. The abstract reports that Alectinib binds C1q with high affinity, but this is mechanistically unexpected sin
CI-generated notebook stub for analysis SDA-2026-04-14-gap-pubmed-20260410-181356-57d1f917. The study shows dramatic functional recovery and muscle re-innervation after cytoplasmic TDP-43 clearance, e
CI-generated notebook stub for analysis SDA-2026-04-16-gap-pubmed-20260411-082446-2c1c9e2d. The abstract explicitly questions whether AD's hallmark pathologies induce cholinergic dysfunction or vice v
CI-generated notebook stub for analysis SDA-2026-04-16-gap-ferroptosis-als-d2fb6bf796ed. Iron-dependent cell death (ferroptosis) as a mechanism in ALS and motor neuron diseases. Focus on GPX4 (glutath
CI-generated notebook stub for analysis SDA-2026-04-16-gap-debate-20260411-065018-92a34465. The debate framework identified synaptic vesicle protein modifications as critical but no specific hypothese
CI-generated notebook stub for analysis SDA-BIOMNI-FINE_MAP-215bc2c6. Can Bayesian fine-mapping of the top 25 AD GWAS loci identify credible sets of causal variants with high posterior probability?
CI-generated notebook stub for analysis SDA-BIOMNI-PROTEOMI-c4a33049. Which proteins are differentially expressed in AD CSF and brain tissue, and do they replicate across independent cohorts (ROSMAP,
CI-generated notebook stub for analysis SDA-BIOMNI-BINDER_D-0657a9ed. Can computational de novo protein binder design produce stable binders that block the alpha-synuclein aggregation interface respon
CI-generated notebook stub for analysis SDA-BIOMNI-POLYGENI-b3028c7a. How well do current AD polygenic risk scores predict disease onset in independent cohorts, and does adding rare variant burden imp
CI-generated notebook stub for analysis SDA-BIOMNI-SURVIVAL-3e217f4d. Which clinical, genetic, and biomarker features are independent prognostic markers for time-to-dementia in cognitively impaired in
CI-generated notebook stub for analysis SDA-BIOMNI-GENE_COE-55fc5237. What co-expression modules are shared and unique across brain regions in AD, and which hub genes in these modules are druggable ta
CI-generated notebook stub for analysis SDA-BIOMNI-SPATIAL_-c2b61633. How does spatial gene expression in the hippocampus and entorhinal cortex distinguish AD pathology stages, and which spatial neigh
CI-generated notebook stub for analysis SDA-BIOMNI-BIOMARKE-34ec007c. Can a multi-modal biomarker panel combining plasma proteins, neuroimaging features, and genetic risk scores outperform individual
CI-generated notebook stub for analysis SDA-2026-04-16-gap-20260416-121711. How do gut microbiome-derived metabolites SCFAs LPS TMAO influence alpha-synuclein aggregation and dopaminergic neuron survi
CI-generated notebook stub for analysis SDA-2026-04-16-gap-pubmed-20260410-192526-f2bbb9ab. While the study demonstrates dose-response relationships between amyloid levels and outcomes, it doesn't est
CI-generated notebook stub for analysis SDA-2026-04-16-gap-pubmed-20260410-170027-a1e5f867. While the study establishes LRRK2 as a lysosomal swelling sensor and notes that lysosomal swelling occurs in
CI-generated notebook stub for analysis SDA-2026-04-15-gap-pubmed-20260406-062118-e3613755. The study shows SPP1 from perivascular cells drives microglial synaptic engulfment, but the specific recepto
CI-generated notebook stub for analysis SDA-2026-04-15-gap-pubmed-20260410-100455-ff18091d. The abstract challenges the rationale for using microtubule-stabilizing drugs in tau diseases, since tau app
CI-generated notebook stub for analysis SDA-2026-04-04-frontier-connectomics-84acb35a. How do structural and functional connectivity changes in the human brain connectome drive cognitive decline in Al
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112522-57d1cc4f. While TREM2 was identified as critical for microglial senescence, the debate lacked fine-grained temporal da
CI-generated notebook stub for analysis SDA-2026-04-04-frontier-proteomics-1c3dba72. What are the critical protein expression changes and post-translational modifications (phosphorylation, ubiquitinat
CI-generated notebook stub for analysis SDA-2026-04-12-gap-debate-20260410-145418-c1527e7b. Why have numerous phase 3 clinical trials failed despite advances in understanding AD pathobiology?
CI-generated notebook stub for analysis SDA-2026-04-09-gap-debate-20260409-201742-1e8eb3bd. The debate mentioned tau PTM targeting but did not identify which modifications are both disease-specific an
CI-generated notebook stub for analysis SDA-2026-04-12-gap-pubmed-20260410-184126-b2c3e2e8. How does APOE4's beneficial immune function reconcile with its established role as the strongest AD risk fac
CI-generated notebook stub for analysis SDA-2026-04-09-gap-debate-20260409-201742-5407d57d. The debate highlighted broad cellular toxicity of existing HSP inhibitors but did not resolve how to enginee
CI-generated notebook stub for analysis SDA-2026-04-16-gap-debate-20260410-113104-a13caf2e. The skeptic raised evidence that APOE4 carriers show enhanced cholesterol synthesis, suggesting the lipid bi
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112441-f2afffb3. The debate raised whether SST/PV interneuron dysfunction represents adaptive compensation to maintain circui
CI-generated notebook stub for analysis SDA-2026-04-09-gap-debate-20260409-201742-ca7016f1. The debate identified vesicle accessibility as a major concern for nanobody approaches but provided no evide
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112400-454036f1. The debate revealed contradictory evidence about CD8+ T cell roles in neurodegeneration, with some studies s
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112330-9abf86eb. The debate identified a critical therapeutic window when astrocytic ketone production declines but neurons r
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112730-24052bbe. The debate highlighted tau prion-like transmission but did not resolve how different tau conformations compe
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112819-e40e0fa2. The debate established that ceramide accumulation affects amyloid-β processing but didn't resolve the spatia
CI-generated notebook stub for analysis SDA-2026-04-09-gap-debate-20260409-201742-d279750b. The debate proposed targeting vesicle surface glycans but acknowledged no published data demonstrates unique
CI-generated notebook stub for analysis SDA-2026-04-12-gap-debate-20260410-113021-6fbc6da4. The debate identified a critical mechanistic gap between SCFA production by gut bacteria and α-synuclein dis
CI-generated notebook stub for analysis SDA-2026-04-12-gap-debate-20260410-113051-5dce7651. The debate highlighted a critical dosing paradox where both hypo- and hypermethylation could be harmful, but
CI-generated notebook stub for analysis SDA-2026-04-15-gap-debate-20260410-112607-0a3749ea. Despite the debate focusing on SEA-AD transcriptomic data, no actual gene expression patterns or pathway ana
CI-generated notebook stub for analysis SDA-2026-04-15-gap-pubmed-20260411-093924-7330920b. The abstract claims C. butyricum-GLP-1 crosses the BBB and binds to GLP-1 receptors, but this is mechanistic
CI-generated notebook stub for analysis SDA-2026-04-12-gap-debate-20260410-112908-13c403ee. The debate revealed conflicting estimates ranging from <5% to 20% for FcRn's role in BBB transport, with spe
CI-generated notebook stub for analysis SDA-2026-04-16-gap-debate-20260410-113045-27c7b314. The debate revealed conflicting evidence about whether TRPML1 activation rescues or worsens lysosomal functi
CI-generated notebook stub for analysis SDA-2026-04-12-gap-debate-20260410-113038-57244485. The debate revealed conflicting evidence about whether connexin-43 mediates mitochondrial transfer through g
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