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).

• Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.

  PMID 41781335 · PMC13138019 · Genome research · 2026 · 8 claims · 8 setups

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  Mutation-based ASE detection in bulk tumor samples can be confounded by gene expression differences between tumor and normal cells, producing apparent enrichment of the mutant allele in RNA without true ASE.

  tcga cutaneous serially whole-exome bulk novo

• Eduomics: a Nextflow pipeline to simulate -omics data for education.

  PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups

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  Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements

  chromosome full simulated exome rna-seq pipeline

• Repurposing public sarcoma multi-omics for neoantigen discovery.

  PMID 42012689 · PMC13100081 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 7 setups

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  Reanalysis of legacy CKS multi-omic data shows that standard genome-wide metrics frequently underestimate the true immunogenic potential of these tumors.

  paired cks peptides whole-exome rna-seq hla

• Determining the quality and complexity of next-generation sequencing data without a reference genome.

  PMID 25514851 · PMC4298064 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  kPAL, an open-source alignment-free package, assesses sequencing data quality and complexity using k-mer frequency profiles and pairwise distances between them, without a reference sequence.

  rna-seq genome wgs exome k-mer rna-seq read