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 13

System / cell line: stromal ✕ Assay: pseudotime ✕ Clear

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

PMID 41811178 · PMC12978698 · eLife · 2026 · 8 claims · 8 setups

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Cell type-specific Bayesian and co-expression networks generated from BMSC-OB scRNA-seq data in Diversity Outbred mice can prioritize and contextualize genes underlying human BMD GWAS associations

bmsc-ob genes mesenchymal gtex scrna-seq cellect iterativewgcna
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

Has reproduction · 65

comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

hipsc-derived combo combo-derived healthy-donor flow single-cell confocal
Generation of thymus-reconstituting T cell progenitors from human pluripotent stem cells.

PMID 41512861 · PMC12853186 · Cell reports methods · 2026 · 7 claims · 6 setups

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A cytokine-free hPSC hematopoietic differentiation protocol followed by OP9-DLL4 stromal co-culture generates pro-T cells without genetic manipulation

hpsc hescs hpsc-hec-derived sorted flow tcr single-cell
Precancerous niche remodelling dictates nascent tumour persistence.

PMID 41781610 · PMC13148994 · Nature · 2026 · 8 claims · 8 setups

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Newly emerging tumours actively remodel their surrounding stroma into a 'precancerous niche' that determines their long-term survival.

upper nascent oesophagus carcinogen-free immunofluorescence edu immune
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
Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

PMID 41837870 · PMC13248853 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 6 setups

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Micropatterned cardioids generated from hiPSCs co-develop mesoderm-heart and endoderm-foregut/liver lineages, including a previously unreported non-neural ectoderm population.

hipsc-derived crispr-engineered micropatterned scrna-seq whole-mount clearing single-cell
Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

PMID 41933362 · PMC13173987 · BioData mining · 2026 · 8 claims · 7 setups

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Single-cell analysis of integrated ovarian cancer datasets identifies 9 distinct mononuclear phagocyte clusters (MPC1-MPC9), of which MPC3, MPC5, and MPC7 are hypermetabolic

ovarian mpc annotated tcga-oc single-cell gene pseudotime
FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.

PMID 41591566 · PMC12847211 · Acta neuropathologica · 2026 · 8 claims · 7 setups

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FAP is consistently upregulated in MPNSTs compared to neurofibromas at the transcript level across independent bulk datasets

archival tcga peripheral nf-1-associated bulk spatial single-cell
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
A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

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Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide
Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

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γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

crc γδt epithelial c4_cxcl13 single-cell differential pseudotime
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

Has reproduction · 85

Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine

Experiments

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations.

comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

Generation of thymus-reconstituting T cell progenitors from human pluripotent stem cells.

Precancerous niche remodelling dictates nascent tumour persistence.

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

Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.

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

A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.