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).

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel reference panel-free, read-based phasing algorithm substantially improves SNV calling accuracy over standard filtering in ONT data.

  na12878 ataxia-pancytopenia simulated whole-genome snv read-based

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 4 setups

  Has reproduction · 50

  TOSCA is the first automated, modular open-source tumor-only somatic calling workflow for whole-exome and targeted panel sequencing, covering raw reads through variant classification.

  t-cell hcc1395 clinical targeted whole-exome

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

  memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc