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).

• SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.

  PMID 41993886 · PMC13082578 · Computational and structural biotechnology journal · 2026 · 6 claims · 6 setups

  Full-text index only

  SnakeAltPromoter is the first unified, reproducible Snakemake workflow that automates alternative promoter analysis from raw RNA-seq data using 3 complementary methods (ProActiv, Salmon, DEXSeq)

  heart brain gm12878 simulated bulk cage rna-seq

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• Calibration-free NGS quantitation of mutations below 0.01% VAF.

  PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 96

  QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

  h37rv repository healthy same single-plex 10-plex 22-plex