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).
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scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.
PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups
scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.
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Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.
PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups
GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model
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Has reproduction · 67
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.
PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups
The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions
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Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.
PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups
446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways