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).

• Integrated drug resistance and leukemic stemness gene-expression scores predict outcomes in large cohort of over 3500 AML patients from 10 trials.

  PMID 39090192 · PMC11294346 · NPJ precision oncology · 2024 · 7 claims · 6 setups

  Has reproduction · 50

  A 5-gene ADE-Resistance Score (ADE-RS5), derived via LASSO regression from 67 pharmacologically relevant genes, predicts MRD positivity, EFS and OS in pediatric AML.

  pediatric combined lasso gene-expression-based integrated

• All of gene expression (AOE): An integrated index for public gene expression databases.

  PMID 31978081 · PMC6980531 · PloS one · 2020 · 6 claims · 4 setups

  Has reproduction

  ArrayExpress (AE) discontinued importing data from GEO in 2017, causing new GEO entries to become unavailable from AE

  geo arrayexpress aoe cross-database metadata keyword

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

  Full-text index only

  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

  PMID 41915012 · PMC13142155 · GigaScience · 2026 · 8 claims · 7 setups

  Full-text index only

  Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

  10x brain ucsc datasets scrna-seq integration snrna-seq

• Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

  PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

  Has reproduction · 68

  scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

  raw real-world expressed gene deep

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Cell neighborhood topology directs rare cell population identification.

  PMID 41912521 · PMC13199379 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  RareQ is a framework that quantifies neighborhood connectivity (Q), a cell-specific measure of kNN-graph cliquishness, to detect rare cell populations from single-cell and spatial omics data

  downsampled pbmc brain simulated scrna-seq cite-seq single-cell