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).

• Extending differential gene expression testing to handle genome aneuploidy in cancer.

  PMID 41894415 · PMC13061324 · PLoS computational biology · 2026 · 8 claims · 4 setups

  Full-text index only

  DeConveil integrates CNV data into DGE analysis using a GLM with negative binomial distribution to correct for CN-driven gene dosage effects

  simulated lung tcga breast simulated bulk

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 8 claims · 7 setups

  Has reproduction · 53

  A computational framework mapping single-cell Z-score expression to matched patient-level CNV data can identify recurrent, cross-cell-type copy-number-driven expression (dosage) events.

  tnbc independent cng-up breast single-cell gene network

• Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

  PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

  Full-text index only

  MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

  gastric epithelial stomach nod-scid single-cell cnv differential

• Molecular profiling of breast cancer in native American women reveals distinct genomic and transcriptomic features.

  PMID 41844957 · PMC13144316 · NPJ precision oncology · 2026 · 8 claims · 6 setups

  Full-text index only

  This is the first multi-omics (mutation, CNV, RNA-seq) characterization of breast tumors from Native American women, providing a resource for future studies

  breast degs targeted panel-derived whole-transcriptome

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy

• Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

  PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

  Full-text index only

  γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

  crc γδt epithelial c4_cxcl13 single-cell differential pseudotime

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

  PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

  Full-text index only

  Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

  validation cns healthy genes methylation copy-number gene-set

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

  PMID 41916296 · PMC13130669 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Immune and stromal heterogeneity, rather than genetic variation, are primary drivers of gene expression ITH in iCCA

  multi-region icca four lihv bulk hallmark single-cell