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 18

System / cell line: malignant ✕ Assay: subtype ✕ Clear

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
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
Single cell profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

PMID 42023148 · PMC13097095 · iScience · 2026 · 8 claims · 8 setups

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PCNSL and sDLBCL contain five distinct malignant B-cell subtypes (B0-B4) with discrete differentiation trajectories

pcnsl malignant bulk sdlbcl scrna-seq infercnv cytotrace2
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

PMID 41723121 · PMC12932787 · Nature communications · 2026 · 8 claims · 8 setups

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Different tumor cell transcriptomic states organize into distinct spatial clusters, or 'villages', each supported by a unique surrounding microenvironment

liver malignant non-malignant tumor single-cell immunofluorescence non-negative
The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

PMID 14580250 · PMC314415 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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ADH and ductal carcinoma in situ (DCIS) are precursor lesions molecularly similar to adjacent invasive breast cancer

locally adh brca1 malignant array chromosome-based cdna
An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC

nsclc epithelial macrophage caf scrna-seq copy gene-set
Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

tumor hnacc epithelial accb single-cell scrna-seq copy
A cellular epigenetic classification system for glioblastoma.

PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

gbm healthy pseudo-bulk tcga illumina single-cell deconvolution
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

pancreatic kpc pdac tcga-paad rna-seq bulk proteomics
Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.

PMID 42066772 · PMC13198276 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Integrative bulk, single-nucleus, and spatial RNA-seq analysis identifies three LME subtypes in MALT lymphoma: LME1 (mesenchymal), LME2 (inflammatory), and LME3 (depleted).

malt ffpe snrna-seq-derived snrna-seq bulk single-nucleus spatial
Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

PMID 15932632 · PMC1177929 · BMC cancer · 2005 · 7 claims · 4 setups

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VHL mutations were detected in 61% (114/187) of sporadic clear-cell RCC patients

archival subset flanking paraffin-embedded pcr-sscp feasibility histopathological
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
Proteomic profiling in ovarian cancer.

PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

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No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

serum tumor rolling mass microarray
Robust and efficient annotation of cell states through gene signature scoring.

PMID 41708334 · PMC12951948 · Genome research · 2026 · 8 claims · 8 setups

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Established scoring methods (Seurat, SCANPY, UCell, JASMINE) fail to provide robust and comparable score distributions across diverse signatures and experimental conditions, precluding accurate unsupervised cell-state annotation.

pbmc colorectal esophageal crc scrna-seq cross-implementation signature
Multi-omics evaluation of cell lines as models for metastatic prostate cancer.

PMID 41876625 · PMC13171877 · Communications biology · 2026 · 8 claims · 8 setups

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Substantial genomic differences exist between metastatic prostate cancer patient samples and prostate cancer cell lines, including hotspot mutations largely absent from cell lines.

prostate metastatic su2c tcga somatic copy bulk
Ovarian cancer biomarkers: current options and future promise.

PMID 18926090 · PMC3381792 · Journal of the National Comprehensive Cancer Network : JNCCN · 2008 · 8 claims · 8 setups

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CA125 lacks the sensitivity and specificity needed for reliable early-stage ovarian cancer detection, since only ~50% of stage I/II cases show elevated levels

serum plasma preoperative advanced serum plasma elisa
Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.

PMID 41001759 · PMC12713092 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 8 claims · 8 setups

Has reproduction

CD146 (MCAM) is a superior surface marker for sorting GBM pericytes, labeling nearly all PDGFRβ+ pericytes with strong specificity, unlike NG2 which labels fewer vessel-associated pericytes.

facs-sorted frozen dissociated scrna-seq scrna-seq immunofluorescence fluorescence-activated
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson

Experiments

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

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

Single cell profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer.

The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.

Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

A cellular epigenetic classification system for glioblastoma.

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.

Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

Proteomic profiling in ovarian cancer.

Robust and efficient annotation of cell states through gene signature scoring.

Multi-omics evaluation of cell lines as models for metastatic prostate cancer.

Ovarian cancer biomarkers: current options and future promise.

Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.