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).

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 8 claims · 5 setups

  Has reproduction · 62

  A DNN model built on 34 top-ranked hub genes achieves the highest prediction accuracy (AUC 92.11%) for distinguishing primary from bone-metastasized tumors

  breast degs geo tcga microarray protein-protein machine

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.

  PMID 41707654 · PMC12923980 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  DeCAF is a single-sample kTSP classifier using 9 TSP gene pairs that predicts proCAF vs restCAF subtypes from bulk expression data

  pdac cptac external elyada-sc bulk single-sample classifier

• PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.

  PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups

  Has reproduction · 40

  NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone

  cd45+ ffpe scrna-seq cd8+ single-cell multiplex gene

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA

  soochow-blca tcga-blca gse13507 gse135337 bulk scrna-seq somatic

• 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

• Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

  PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Full-text index only

  Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

  pca tcga-prad external scrna-seq bulk immune