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 832

System / cell line: cancer ✕ Clear

ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.

PMID 41888873 · PMC13154904 · Genome biology · 2026 · 8 claims · 6 setups

Full-text index only

ImmuSeeker leverages the phylogenetic structure of HLA/KIR alleles in its alignment and filtering strategy to improve accuracy and robustness of immune gene signature detection

a549 rna-seq covid-19 autoimmune bulk iso-seq rna-seq
X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancer.

PMID 41922576 · PMC13099652 · Oncogene · 2026 · 8 claims · 8 setups

Full-text index only

lncRNA1456, previously classified as noncoding, encodes a 132 amino acid protein named XCP (X-linked Cancer-associated Polypeptide)

mcf-7 breast recombinant polya+ lc-ms race
Nested co-expression network analysis identifies compact gene clusters in a black box.

PMID 41934621 · PMC13163169 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

Full-text index only

Nested-WGCNA is a two-stage algorithm that identifies coarse-grained modules (CGMs) and then, via core decomposition and renormalization, derives fine-grained modules (FGMs) representing subprocesses within each CGM

tcga-blca tcga-kirc tcga-luad imvigor210 bulk scrna-seq
Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.

PMID 41942785 · PMC13053443 · Journal of molecular medicine (Berlin, Germany) · 2026 · 8 claims · 8 setups

Full-text index only

A PDAC-enriched myoCAF-c1 fibroblast cluster is closely associated with epithelial-mesenchymal transition (EMT) and angiogenesis

pdac myocaf-c1-derived tcga-paad scrna-seq spatial bulk
PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

PMID 41951588 · PMC13237225 · Nature communications · 2026 · 8 claims · 6 setups

Full-text index only

Progenitor-exhausted CD8+ T cells (CD8-Tpex, TCF7+PDCD1+) are enriched in proximal lymph nodes and proliferate at a high rate after ICI treatment

esophagogastric cancer surgically tcga scrna-seq scrna reanalysis
Podoplanin-defined tumour plasticity and CCR7-mediated lymphatic metastasis in triple-negative breast cancer.

PMID 41957138 · PMC13226698 · British journal of cancer · 2026 · 8 claims · 8 setups

Full-text index only

A PDPN-defined tumour cell mesenchymal shift, promoted by hypoxia, is required for efficient CCR7-driven lymphatic metastasis and tumour progression

eo771 c57bl tnbc tumour proliferation tumour flow
Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer.

PMID 41978385 · PMC13076935 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

Full-text index only

scMnT identifies MSI cells and quantifies MSI intensity at single-cell resolution from scRNA-seq data using mononucleotide microsatellite allele length statistics

crc cancer sc035 p20 scrna-seq snv msi
BCG-trained macrophages promote pan-anti-tumor activity through epigenetic rewiring of NOX2-ROS axis.

PMID 42032669 · PMC13261971 · Journal of experimental & clinical cancer research : CR · 2026 · 7 claims · 8 setups

Full-text index only

BCG training induces pan-anti-tumor activity across multiple mouse tumor models, mediated predominantly by tumor-associated macrophages (TAMs)

llc tumor-infiltrating macrophage raw264.7 tumor flow antibody-mediated
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
Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

PMID 42062553 · PMC13259927 · Nature methods · 2026 · 8 claims · 6 setups

Full-text index only

Xenium data show strong consistency across patients and technical replicates, with little technical variation between platforms

ffpe matched xenium xenium single-nucleus immunohistochemistry
A Cisplatin-Based Prodrug Inhibits Nucleotide Excision Repair Independently of Chromatin Accessibility to Overcome Resistance.

PMID 42072663 · PMC13113776 · Biomolecules · 2026 · 6 claims · 6 setups

Full-text index only

cPVP, a novel Pt(IV) prodrug combining cisplatin with the KDAC inhibitors phenylbutyrate (PhB) and valproic acid (VPA), induces significantly greater cytotoxicity and DNA damage than cisplatin alone

a2780 mtt icp-ms damage-seq
EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets.

PMID 42097304 · PMC13186194 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

Full-text index only

EMTscore is an R package providing efficient, unbiased scoring of multiple EMT pathways from single-cell or bulk omics data

small a549 trunk bulk scrna-seq
InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.

PMID 42109251 · PMC13158666 · Nucleic acids research · 2026 · 8 claims · 6 setups

Full-text index only

InSituPREP is a computational framework that quantifies proximity-associated gene programs across multiple analytical layers (binary contacts, graded distance, density, triplets, RNA velocity) in 3D single-cell spatial data

breast adjacent exseq-imaged exseq-derived expansion 16s scrna-seq
A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

PMID 42111187 · PMC13157187 · iScience · 2026 · 8 claims · 8 setups

Full-text index only

cfDNAanalyzer integrates feature extraction, feature processing/selection, and machine learning model building into a single one-command-line toolkit for cfDNA genomic sequencing data

balanced breast healthy multi-cancer cfdna machine computational
Infrequent involvement of p53 gene mutations in the tumourigenesis of Japanese prostate cancer.

PMID 7691145 · PMC1968625 · British journal of cancer · 1993 · 6 claims · 3 setups

Full-text index only

p53 gene mutations are infrequent in the tumorigenesis of primary Japanese prostate cancer

prostate pcr-sscp sequencing
PRLTS gene alterations in human prostate cancer.

PMID 9197531 · PMC5921422 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 3 setups

Full-text index only

LOH at the PRLTS gene locus is a relatively common abnormality in prostate cancer

tumor metastatic loh pcr-sscp sequencing
Molecular analysis of the BRCA1 and BRCA2 genes in 32 breast and/or ovarian cancer Spanish families.

PMID 10755399 · PMC2374482 · British journal of cancer · 2000 · 8 claims · 3 setups

Full-text index only

Only 25% (8/32) of the Spanish breast/ovarian cancer families carried a BRCA1 or BRCA2 mutation

genomic truncation single-strand direct
Mutations of the BRCA1 and BRCA2 genes in patients with bilateral breast cancer.

PMID 11556836 · PMC2375067 · British journal of cancer · 2001 · 7 claims · 3 setups

Full-text index only

BRCA1 and BRCA2 mutations are not significantly more prevalent in patients with bilateral breast cancer than in matched unilateral controls

genomic clinical pcr-sscp restriction kaplan-meier
Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

Full-text index only

RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

colorectal same pcr-based msi
Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

PMID 11985787 · PMC5927018 · Japanese journal of cancer research : Gann · 2002 · 6 claims · 3 setups

Full-text index only

MN mutations occur significantly more frequently in sporadic colorectal cancer (56%) than in gastric cancer (25%)

sporadic same multilocus pcr-simple

Experiments

ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.

X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancer.

Nested co-expression network analysis identifies compact gene clusters in a black box.

Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.

PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

Podoplanin-defined tumour plasticity and CCR7-mediated lymphatic metastasis in triple-negative breast cancer.

Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer.

BCG-trained macrophages promote pan-anti-tumor activity through epigenetic rewiring of NOX2-ROS axis.

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

Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

A Cisplatin-Based Prodrug Inhibits Nucleotide Excision Repair Independently of Chromatin Accessibility to Overcome Resistance.

EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets.

InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.

A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

Infrequent involvement of p53 gene mutations in the tumourigenesis of Japanese prostate cancer.

PRLTS gene alterations in human prostate cancer.

Molecular analysis of the BRCA1 and BRCA2 genes in 32 breast and/or ovarian cancer Spanish families.

Mutations of the BRCA1 and BRCA2 genes in patients with bilateral breast cancer.

Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.