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 29

System / cell line: cohort ✕ Assay: cnv ✕ Clear

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
Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

PMID 41840060 · PMC13125306 · Scientific reports · 2026 · 8 claims · 7 setups

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IDC exhibits significantly higher CNV burden than DCIS, supporting progressive genomic instability during tumor evolution

her2-positive epithelial malignant tcga-brca single-cell spatial infercnv
Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

PMID 41916296 · PMC13130669 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Immune and stromal heterogeneity, rather than genetic variation, are primary drivers of gene expression ITH in iCCA

multi-region icca four lihv bulk hallmark single-cell
Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

crc epcam+ aggregated cancer scrna-seq copy pseudobulk
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

representative illumina six snp serial concentration
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
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
The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

PMID 42011021 · PMC13096693 · Clinical and translational medicine · 2026 · 6 claims · 8 setups

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KRAS-mutant LUAD patients show significantly poorer pathological response and inferior long-term survival after neoadjuvant immunotherapy compared to KRAS-wildtype patients

resected resectable epithelial cd4t_treg_tnfrsf4 scrna-seq retrospective cnv
Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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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
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

Has reproduction · 77

457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy
A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

crc epithelial rcrc tcga-read scrna-seq copy gene
Dasatinib resensitizes BRAF/MEK inhibitor efficacy in patient-derived xenografts from patients with progression on BRAF/MEK inhibitor treatment.

PMID 41704766 · PMC12907876 · iScience · 2026 · 8 claims · 6 setups

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Genomic mutation and copy-number status show weak correlation with total/phospho-protein expression and pathway activation in melanoma PDX and TCGA samples

pdx discovery cutaneous nsg reverse-phase targeted rppa
KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

PMID 41907411 · PMC13018899 · iScience · 2026 · 8 claims · 8 setups

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A malignant epithelial subpopulation (Cluster 0) with the highest CytoTRACE stemness potential and highest EMT activity exists in ESCC scRNA-seq data

escc degs eca109 kyse180 scrna-seq machine immunohistochemistry
Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

PMID 42034645 · PMC13247122 · Cell death & disease · 2026 · 8 claims · 8 setups

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Single-cell profiling of BCBM identifies 12 tumor-associated macrophage (TAM) subtypes and 5 metastatic tumor cell (MTC) subtypes with distinct transcriptional profiles

brain breast scrna-seq tams scrna-seq bulk copy
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

Has reproduction · 85

High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

breast er+ epithelial malignant scrna-seq spatial copy
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

Has reproduction · 93

m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis

tcga aml gse12417 bulk mutation methylation
Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

Has reproduction · 96

A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

gastric gene scrna-seq tcga single-cell wgcna cell-cell
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

Has reproduction

Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

tcga same metastatic tumor-only whole-exome wes copy-number
Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

luad pan-cancer tumor scrna-seq spatial bulk

Experiments

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

Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.

Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

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

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

The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

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

Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

Dasatinib resensitizes BRAF/MEK inhibitor efficacy in patient-derived xenografts from patients with progression on BRAF/MEK inhibitor treatment.

KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.