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 20

System / cell line: epithelial ✕ Assay: paired ✕ Clear

Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

lung scanned excised peptide 2-d 2-de maldi-tof-ms
Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

PMID 7577492 · PMC2033953 · British journal of cancer · 1995 · 7 claims · 4 setups

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LOH analysis has higher sensitivity than DNA flow cytometry for detecting unifocal origin of bilateral ovarian tumors

bilateral paraffin-embedded ovarian peripheral loh flow isolation
Colorectal microenvironment determines the prognosis of colorectal cancer.

PMID 41495419 · PMC12868731 · Experimental & molecular medicine · 2026 · 8 claims · 7 setups

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The colorectal microenvironment (classified via NBT gene expression as tumor-supportive vs healthy) can serve as a prognostic biomarker predicting cancer invasiveness and recurrence

paired nbt slide bulk bulk 16s 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
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

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A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

ovarian case matched same pcr-sscp subcloning loh
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 80

BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

lung known leukemia tumor paired-end computational snp
Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

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Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

breast real colon tcga paired pseudobulk bulk
Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

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A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

escc gse53625 gse160269 imvigor210 microarray univariate single-cell
AJUBA: The Master Regulator Bridging EMT and Immune Evasion in Colorectal Cancer.

PMID 41814682 · PMC13140425 · Mediators of inflammation · 2026 · 8 claims · 8 setups

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AJUBA is markedly upregulated in CRC across multiple transcriptomic cohorts and is enriched in epithelial cells with activated EMT features

tcga-crc crc paired hct116 bulk single-cell spatial
PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer.

PMID 41932868 · PMC13172513 · Cell death & disease · 2026 · 8 claims · 8 setups

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PMEPA1 is a pivotal EMT regulator in BTC; its high expression correlates with adverse prognosis and distant metastasis

btc tcga hucct1 scrna-seq cnmf bulk
UBE2M as a bridge spanning neddylation and cell cycle regulation in colorectal adenocarcinoma.

PMID 41680469 · PMC12993059 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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Neddylation is associated with G2M phase progression in CRC

crc paired hek293t cell-free single-cell bulk immunohistochemistry
Prophylactic Inhaled Pattern Recognition Receptor Agonists Reprogram Lung Epithelial Response and Prevent Type 2 Allergic Inflammation.

PMID 41891295 · PMC13022946 · European journal of immunology · 2026 · 8 claims · 7 setups

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Pam2ODN pretreatment reduces airway Th2 polarization and eosinophilic inflammation without affecting Th1, Th17, or Treg responses

balf lung mediastinal facs-sorted flow bulk scrna-seq
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 71

CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.

unstimulated cd4+ kidney liver bulk single-cell
Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

PMID 42098796 · PMC13154700 · Microbiome · 2026 · 8 claims · 5 setups

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Poly(A)-enriched mRNA-seq can reliably reconstruct microbiome composition, validated against a quantitative mock community standard and metagenomic analysis

zymobiomics vls-vscc vulvar subset mrna-seq rna-seq poly
Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

Has reproduction · 73

N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence
A global view of protein expression in human cells, tissues, and organs.

PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised
sCellST predicts single-cell gene expression from H& E images.

PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

ovarian kidney prostate breast simulation spot-level nucleus
Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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LUSC arising within UIP originates from AT2-derived metaplastic basal cells

fresh-frozen same scrna-seq paired single-cell copy ligand-receptor
Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

tcga-luad geo lung single-cell bulk ssgsea cibersort

Experiments

Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

Colorectal microenvironment determines the prognosis of colorectal cancer.

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

Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

AJUBA: The Master Regulator Bridging EMT and Immune Evasion in Colorectal Cancer.

PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer.

UBE2M as a bridge spanning neddylation and cell cycle regulation in colorectal adenocarcinoma.

Prophylactic Inhaled Pattern Recognition Receptor Agonists Reprogram Lung Epithelial Response and Prevent Type 2 Allergic Inflammation.

Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.

Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

A global view of protein expression in human cells, tissues, and organs.

sCellST predicts single-cell gene expression from H& E images.

Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.