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 16

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

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative
Ectopic CD11c Drives SMAD3-Mediated Aberrant Antigen Presentation and Epithelial-Mesenchymal Transition in Esophageal Squamous Cell Carcinoma.

PMID 41799568 · PMC12963642 · Cancer communications (London, England) · 2026 · 8 claims · 13 setups

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An ESCC epithelial cell subcluster with ectopic CD11c (ITGAX) expression, found in both mice and humans, exhibits concurrent impaired antigen presentation and EMT phenotypes

4-nqo-induced escc esophageal lung multiplex flow whole-genome
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
Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

PMID 41845425 · PMC13104401 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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A LAMA3+ epithelial subpopulation (C3) enriched at the invasive tumor front shows strong EMT signatures and is associated with poor prognosis

escc epithelial scrna-seq tcga-escc scrna-seq spatial infercnv
Uropathogenic Escherichia coli invade luminal prostate cells via FimH-PPAP receptor binding.

PMID 41507584 · PMC12872464 · Nature microbiology · 2026 · 8 claims · 8 setups

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A 2D mouse stem cell-derived prostate epithelial organoid model was developed that mimics epithelial heterogeneity of the murine prostate

prostate bladder immunofluorescence single-cell transepithelial
Defining disease with laser precision: laser capture microdissection in gastroenterology.

PMID 18619446 · PMC3736118 · Gastroenterology · 2008 · 8 claims · 8 setups

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LCM allows isolation of pure cell populations from heterogeneous tissue without damaging DNA, RNA, or protein integrity.

esophagus gastric colorectal colonic maldi cdna profiling
Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk
FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment.

PMID 41904157 · PMC13195071 · Nature communications · 2026 · 7 claims · 8 setups

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Prostate-specific Foxa1 deletion in Pten-null mice drives tumor progression by reprogramming luminal PCa cells toward a basal/squamous-like de-differentiated state

prostate epithelial colony lymph h&e immunohistochemistry 10x
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

patients bulk colorectal epithelial clinical bulk single-cell
TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups

Has reproduction · 79

TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.

cervical tcga-cesc hela scrna-seq scrna-seq wgcna cox
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

Has reproduction · 73

COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

coad consensus cibersort mcp-counter
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 80

WGCNA identified 214 key genes in the blue module most correlated with LUAD

tcga-luad merged tedc2-associated a549 wgcna differential machine
Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups

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Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence

albicans hep-2 rhe blood phenotypic growth adhesion
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
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime

Experiments

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

Ectopic CD11c Drives SMAD3-Mediated Aberrant Antigen Presentation and Epithelial-Mesenchymal Transition in Esophageal Squamous Cell Carcinoma.

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

Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

Uropathogenic Escherichia coli invade luminal prostate cells via FimH-PPAP receptor binding.

Defining disease with laser precision: laser capture microdissection in gastroenterology.

Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment.

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

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

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.