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).

• Machine learning-predicted chromatin organization landscape across pediatric tumors.

  PMID 41904260 · PMC13039956 · Scientific reports · 2026 · 8 claims · 5 setups

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  SuPreMo-Akita (built on the Akita CNN) enables systematic in silico prediction of somatic SV effects on 3D genome folding across large SV cohorts where experimental testing is infeasible

  somatic per-sample tumor paired mutagenesis dimensionality h3k27ac

• Detection of alternative splicing: deep sequencing or deep learning?

  PMID 41520225 · PMC12790623 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  Sequence-based deep learning tools (AlphaGenome, SpliceAI, DeepSplice) show potential for initial hypothesis development and as additional filters in standard RNA-seq pipelines, especially when sequencing depth is limited.

  dilated dcm sequence subsampled bulk rna-seq deep

• Improving melanoma classification by integrating genetic and morphologic features.

  PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

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  BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

  archival same subset patients histopathological mutation quantitative