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: single-cell ✕ Assay: probability ✕ Clear

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

first-trimester decidual spots dnk 10x h&e type
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
Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

PMID 41643060 · PMC13073339 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

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Testicular endothelial cells (TECs) function as a central signaling hub coordinating intercellular communication within the human testicular interstitium

testicular testis leydig diabetic single-cell integrative cell-cell
SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

prostate gwas eqtl bph single-cell mendelian bayesian
Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

PMID 41746282 · PMC12998610 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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dominoSignal extends the Domino algorithm to enable statistical testing of differential cell-cell signaling between experimental conditions.

single-cell simulated pdac per-sample single-cell simulation cell-cell
Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

PMID 34576874 · PMC8467633 · Microorganisms · 2021 · 7 claims · 7 setups

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Amitosis causes random assortment of somatic alleles (IESs) in the highly polyploid Paramecium macronucleus, which can be tracked without phenotypic markers using scDNA-seq.

paramecium tetraurelia telomere-capped simulated single-cell bulk bias
Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

PMID 41364805 · PMC13012255 · Blood cancer discovery · 2026 · 7 claims · 8 setups

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IFN-γ signaling after autologous stem cell transplant (ASCT) is associated with markers of impaired CD8+ T-cell memory phenotype

cd138neg cd138pos bone cd8+ single-cell bulk whole-genome
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
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
Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

tcga-brca senescent normal single-cell machine univariate gene
Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.

PMID 33723257 · PMC7961017 · Nature communications · 2021 · 7 claims · 7 setups

Has reproduction · 70

Proportions of activated and proliferating CD8+ T cells (cluster C16/activated EM) are significantly higher in responders before and during therapy

pbmc cd3+cd8+ pbmc-derived metastatic high-dimensional single-cell polychromatic
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

Has reproduction · 85

EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

gene same randomized publicly racipe stochastic randomized
Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

PMID 41540382 · PMC12892679 · Clinical proteomics · 2026 · 8 claims · 8 setups

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PWAS integrating RA GWAS with ARIC and INTERVAL plasma pQTL data identified 35 genetically regulated proteins (42 associations) significantly associated with RA risk.

plasma shared gtex blood proteome-wide two-sample bayesian
CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

species gm12878 types chromatin cross-protein cross-cell-type
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

Experiments

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

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

Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

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

Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

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