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 27

System / cell line: spatial ✕ Assay: survival ✕ Clear

Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell
Spatial single-cell analysis reveals tumor microenvironment signatures predictive of oral cavity cancer outcome.

PMID 41707652 · PMC12923947 · Cell reports. Medicine · 2026 · 8 claims · 6 setups

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Proliferating (KI67+) PROX1+ lymphatic endothelial cells (LECs) at the tumor invasive margin are a strong independent adverse prognostic factor for recurrence-free and overall survival in early-stage OSCC

ffpe lymphatic representative oscc imaging ki67+prox1+ transcriptomic
Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 8 claims · 8 setups

Has reproduction · 64

COL6A3+ TAFs are a distinct matrix-fibroblast subset significantly enriched in non-responders to neoadjuvant antiangiogenic+ICB combination therapy

gbm ffpe col6a3+ thp-1 scrna-seq spatial multiplex
TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

PMID 41666923 · PMC12923953 · Cell reports. Medicine · 2026 · 8 claims · 5 setups

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Tumors stratify into lymphoid-enriched, myeloid-enriched, and mixed immune-infiltrated subtypes independent of oncogenic driver status

resected luad cd4+ multiplex spatial image
Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

tcga-brca gse96058 brca breast bulk single-cell spatial
Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

Has reproduction · 83

AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

stage patients tumour whole-tumour radiomics bulk cellular
Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

colorectal colon patients bulk single-cell spatial bulk
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

facs-sorted same integrated fgf9 hi-c chip-seq metaloci
HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

PMID 41764165 · PMC13065825 · Nature communications · 2026 · 8 claims · 5 setups

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HRCHY-CytoCommunity is an end-to-end graph neural network framework that jointly identifies multi-level (coarse tissue compartment and fine cellular neighborhood) tissue structures from cell-type spatial maps using differentiable graph pooling, adaptive edge pruning, and consistency/balance regularization.

healthy colorectal simulated breast codex visium merfish
scSurv: a deep generative model for single-cell survival analysis.

PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

simulated tcga melanoma renal scrna-seq bulk single-cell
Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

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Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

trp53-null complete t12 cell-deficient imaging survival tumor
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
The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

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CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

healthy tcga luad til-b flow bulk single-cell
Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

malignant tumor csc six single-cell spatial copy
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
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

Has reproduction · 95

Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

breast-cancer-specific tcga ccle four single-sample survival genome-wide
Statistical challenges in preprocessing in microarray experiments in cancer.

PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

lung beer individual outlier expression rank-covariance quality-control
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
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

Has reproduction · 50

Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

hnscc tcga-hnscc caf fibroblast single-cell bulk spatial
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

Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

Spatial single-cell analysis reveals tumor microenvironment signatures predictive of oral cavity cancer outcome.

Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

scSurv: a deep generative model for single-cell survival analysis.

Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

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

The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

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

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

Statistical challenges in preprocessing in microarray experiments in cancer.

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

Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

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