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).

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

  compendium ffpe simulated frna-seq statistical bulk integrity

• Loss of long-range co-expression is a common feature in cancer.

  PMID 41935098 · PMC13247121 · NPJ systems biology and applications · 2026 · 8 claims · 7 setups

  Full-text index only

  In cancer, the strongest co-expressed gene pairs (top MI values) are predominantly intra-chromosomal, unlike in normal tissue.

  tissues same bladder cancer bulk differential bootstrap

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability