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 783

Assay: tumor ✕ Clear

Establishment of a canine urothelial carcinoma-derived organoid biobank: A platform for comparative and translational research.

PMID 41889014 · PMC13140855 · Clinical and translational medicine · 2026 · 8 claims · 6 setups

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Canine urothelial carcinoma closely resembles human muscle-invasive bladder cancer in histopathology, molecular features, biological behavior, metastatic patterns, therapeutic response, and clinical outcome

canine matched paired urine immunohistochemistry bulk single-nuclei
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

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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
Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

PMID 41923619 · PMC13130694 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A 315-gene 'NE-like signature' (NE-like Sig), derived from the WGCNA MEmidnightblue module, marks a lineage-plasticity-associated transcriptional program distinct from canonical NE differentiation.

cases in-house bladder nebc wgcna single-cell spatial
Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

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A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

hnscc ffpe syngeneic independent single-cell multiplexed tumor
Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.

PMID 41925746 · PMC13046951 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 8 setups

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A three-step computational framework (ImmCeRNA) identified 6,070 immune-related ceRNA interactions across 27 cancer types by integrating expression correlation and experimental validation data.

cancer pan-cancer single lung bulk database single-cell
Helicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment.

PMID 41934579 · PMC13199538 · Discover oncology · 2026 · 8 claims · 8 setups

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CFAP73 is progressively downregulated during HP infection and is the top-ranked predictor among nine HP-suppressed genes associated with favorable gastric cancer survival

gastric tcga-stad tcga t-cell–tumor jonckheere-terpstra survival random
Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

PMID 41948931 · PMC13134724 · JCI insight · 2026 · 8 claims · 8 setups

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KIFC1 is overexpressed in SCLC compared with normal tissues and other cancer types

sclc h146 clinical cancer immunofluorescence viability flow
Glioblastoma invasion into different organoid hosts reveals cell-intrinsic and proliferative migratory programs.

PMID 41959666 · PMC13059114 · iScience · 2026 · 8 claims · 8 setups

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GB cells invade both neural and endodermal organoid hosts (lineage-independent), whereas non-malignant neural progenitor cells show markedly reduced infiltration

gbm1 gfp-gbm1 facs-sorted post-invasion image-based immunofluorescence single-cell
Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

PMID 41975179 · PMC13250061 · Nature communications · 2026 · 8 claims · 8 setups

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Epithelial cells in mLNs and matched mLN+ primary tumors (mLN+PTs) show enhanced cancer stemness (higher CytoTRACE scores) compared to mLN-negative and normal samples.

patient-matched mln epithelial tcga-luad scrna-seq spatial cytotrace
Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer.

PMID 41986344 · PMC13083995 · Nature communications · 2026 · 8 claims · 8 setups

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BRAFi (vemurafenib) treatment drives BRAF-mutant melanoma cells through a reversible dedifferentiation transition from a melanocytic state through a neural crest-like state to a drug-tolerant mesenchymal state

m397 patient-derived longitudinal time-series atac-seq chip-seq
A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

PMID 42014663 · PMC13230468 · Discover oncology · 2026 · 8 claims · 8 setups

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A 23-gene PARPi-sensor transcriptomic model stratifies ovarian cancer patients into high- and low-risk groups with significantly different overall survival, validated in TCGA and ICGC cohorts

pdx tcga prognostic tcia bulk non-negative univariate
Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

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

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

ffpe matched xenium xenium single-nucleus immunohistochemistry
Development of predictive models for the prognosis of triple-negative breast cancer using multiple transcriptomic analyses.

PMID 42081506 · PMC13138617 · PloS one · 2026 · 7 claims · 6 setups

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Developed TNBC prognosis predictive models (CoxPH-based) achieving predictive performance exceeding 0.94 AUC, surpassing all prior published TNBC prognosis models (max prior AUC ~0.85)

tcga-brca gse65216 mda-mb-231 metabric bulk microarray rna-seq
Decoding drug-responsive cell subpopulations in triple-negative breast cancer using single-cell multiomics.

PMID 42088352 · PMC13138057 · iScience · 2026 · 8 claims · 8 setups

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A multimodal framework bridging bulk and single-cell transcriptomics data identifies drug-responsive cell subpopulations in TNBC

tnbc tcga mdamb453 hcc1937 bulk scrna-seq crispr
A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups

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A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.

simulated fibroblast breast simulation array
scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

Has reproduction · 62

scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

panglaodb cancer geo gse137829 single-cell bulk
SpaPheno: linking spatial transcriptomics to clinical phenotypes with interpretable machine learning.

PMID 41975540 · PMC13185361 · Genome medicine · 2026 · 8 claims · 8 setups

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SpaPheno integrates spatial transcriptomics with clinically annotated bulk RNA-seq to identify spatially resolved biomarkers predictive of patient outcomes including survival, tumor stage, and immunotherapy response

cortex liver clear breast spatial elastic
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

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

sporadic same multilocus pcr-simple
Have microarrays failed to deliver for developmental biology?

PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

drosophila caenorhabditis developing xenopus cdna genome-wide microarray
DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

tcga-luad tcga luad dendritic-cell bulk survival pan-cancer

Experiments

Establishment of a canine urothelial carcinoma-derived organoid biobank: A platform for comparative and translational research.

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.

Targeting TPX2-dependent lineage plasticity by CDK4/6 inhibition reverses therapy resistance in neuroendocrine bladder carcinoma.

Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.

Helicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment.

Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

Glioblastoma invasion into different organoid hosts reveals cell-intrinsic and proliferative migratory programs.

Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer.

A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

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

Development of predictive models for the prognosis of triple-negative breast cancer using multiple transcriptomic analyses.

Decoding drug-responsive cell subpopulations in triple-negative breast cancer using single-cell multiomics.

A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

SpaPheno: linking spatial transcriptomics to clinical phenotypes with interpretable machine learning.

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

Have microarrays failed to deliver for developmental biology?

DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.