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).

• Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

  PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 5 setups

  Has reproduction · 94

  EiaD is a reproducible, versioned RNA-seq transcriptome dataset combining 916 healthy human eye samples and 1375 GTEx body samples across 19 eye and 54 body tissues, built with a Snakemake pipeline and served as a single SQLite database.

  gtex eye stem retinal bulk differential single-cell

• Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

  PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

  Full-text index only

  HERV expression differs between primary and metastatic cutaneous melanoma

  tcga-skcm metastatic normal selected bulk consensus orf

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

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

  Full-text index only

  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

• pyrpipe: a Python package for RNA-Seq workflows.

  PMID 34085037 · PMC8168212 · NAR genomics and bioinformatics · 2021 · 8 claims · 3 setups

  Has reproduction · 79

  pyrpipe enables development of flexible, reproducible, and easy-to-debug RNA-Seq computational pipelines purely in Python, in an object-oriented manner

  circulating zea bulk novo

• Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

  PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups

  Has reproduction · 51

  Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level

  oncomine tcga-lihc gse89377 hcc pan-cancer bulk microarray