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).

Publications 1.3k Datasets 392.5k Experiments 6

System / cell line: scrna-seq ✕ Assay: machine-learning ✕ Clear

Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 8 claims · 8 setups

Has reproduction · 64

COL6A3+ TAFs are a distinct matrix-fibroblast subset significantly enriched in non-responders to neoadjuvant antiangiogenic+ICB combination therapy

gbm ffpe col6a3+ thp-1 scrna-seq spatial multiplex
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

Has reproduction · 81

scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 63

Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups

Has reproduction · 42

PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.

paad degs bulk consensus tumor
Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

Full-text index only

RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted

Experiments

Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.