Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 6

System / cell line: cell-type-specific ✕ Assay: mutation ✕ Clear

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

Has reproduction · 93

m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis

tcga aml gse12417 bulk mutation methylation
Characterizing gene perturbations in single cells via network divergence analysis.

PMID 41965857 · PMC13249949 · Nature communications · 2026 · 8 claims · 8 setups

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scDNS quantifies gene-specific functional perturbations by measuring Jensen-Shannon divergence between condition-specific gene interaction network configurations

ipsc-derived embryonic panc-1 triple scrna-seq single-nucleus
Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

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Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

brain hippocampus neuronal bulk trade gene
Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

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SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

pdac bulk ssgsea differential
Multiomic and functional validation of ACSL3, a regulator of fatty acid metabolism, as a lymph node metastasis-associated gene in lung adenocarcinoma.

PMID 41998631 · PMC13261843 · Respiratory research · 2026 · 8 claims · 8 setups

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A five-gene FAM-related risk signature (ACSL3, MCAT, NDUFAB1, OLAH, ACSL4)-derived FScore stratifies LUAD prognosis across multiple independent cohorts

tcga-luad luad a549 lymphatic bulk scrna-seq spatial

Experiments

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

Characterizing gene perturbations in single cells via network divergence analysis.

Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

Multiomic and functional validation of ACSL3, a regulator of fatty acid metabolism, as a lymph node metastasis-associated gene in lung adenocarcinoma.