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 624

Assay: scrna ✕ Clear

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
Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

PMID 41842971 · PMC13132380 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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PRC2i/EZH2i alone or combined with AR inhibitors induce diverse cell state programs (CSPs) that increase tumor cell invasion, metastasis, and drug resistance despite only modest suppression of tumor growth.

lncap pca pdx clinical viability tumor ic50
Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

PMID 41844163 · PMC13030975 · Cell reports methods · 2026 · 8 claims · 7 setups

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Cell lysis (CL) nuclei isolation yields substantially more nuclei and less biased immune cell proportions than mechanical separation (MS)

frozen paxgene cl-derived thawed single-nucleus confocal brightfield
Single-cell transcriptome analysis reveals DNMT1(+) epithelial cells promote lymphatic metastasis via CXCL17-mediated TAM infiltration.

PMID 41845371 · PMC13107741 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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DNMT1+ epithelial cells, characterized by high epithelial-mesenchymal transition potential, show a propensity for lymph node metastasis in bladder cancer

bladder scrna-seq um-uc-3 genomic single-cell cell-cell western
DAESC + : high-performance, integrated software for single-cell allele-specific expression data.

PMID 41851619 · PMC13169709 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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DAESC+ is a dual-module, end-to-end software package (DAESC-P for preprocessing, DAESC-GPU for differential analysis) for single-cell ASE data

onek1k endoderm simulated single-cell differential runtime
Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma.

PMID 41854876 · PMC13038760 · Cellular and molecular life sciences : CMLS · 2026 · 8 claims · 8 setups

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STMN1+ and AFP+ malignant cell subsets are enriched in AFP-positive HCC, while CYP3A4+ malignant cells are enriched in AFP-negative HCC

hcc tcga-lihc scrna-seq immunotherapy single-cell bulk spatial
Tumors located in the brain impair the frequency and phenotype of dendritic cells in blood and tumor.

PMID 41858880 · PMC12997301 · iScience · 2026 · 8 claims · 5 setups

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Total circulating DC frequency is significantly reduced in patients with brain tumors compared to healthy donors

pbmcs plasma recurrent dissociated flow elisa scrna-seq
Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis.

PMID 41862476 · PMC13004862 · Nature communications · 2026 · 7 claims · 8 setups

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Mechanical stress (MS) signaling is significantly elevated in endothelial cells (ECs) from IPF patients and correlates with fibrosis severity and lung function decline

lung cd31+ single-nucleus scissor meta-analysis
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea.

PMID 41867623 · PMC13000480 · iScience · 2026 · 8 claims · 8 setups

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GER cells regenerate IPhCs through both mitotic and non-mitotic mechanisms

neonatal lgr5dtr ki67creert2 epcam+ whole-mount edu genetic
Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.

PMID 41873503 · PMC13044578 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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Dark gene families in corals form cosmopolitan (broadly shared) families that originated via bursts of lineage-specific duplication, often from genes with known function

genome same montipora stylophora orthogroup busco bulk
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
The macrophage entry mechanism of SARS-CoV-2 mediated by surface CD98/TMPRSS11E complex is associated with the cellular tropism toward proinflammatory M1 and pathogenesis.

PMID 41877147 · PMC13137717 · Respiratory research · 2026 · 8 claims · 8 setups

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CD98 (CD98hc/SLC3A2) is a novel receptor for the SARS-CoV-2 Spike protein

thp-1-derived 293t structures thp-1 co-ip co-immunoprecipitation molecular
OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

PMID 41877167 · PMC13011277 · Chinese medicine · 2026 · 8 claims · 8 setups

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Eight AS-associated hub genes were identified through integration of multi-omics datasets (DEG analysis, WGCNA, scRNA-seq, Mendelian randomization, PPI module analysis)

gtex as-associated tcm representative differential weighted single-cell
Dysregulated NK-cell gene expression defines the enduring symptoms of long COVID-19.

PMID 41878441 · PMC13006230 · Frontiers in immunology · 2026 · 8 claims · 5 setups

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LTCS patients retain elevated anti-SARS-CoV-2 IgG (spike S1/RBD/N) titers relative to healthy controls despite ongoing symptoms, for up to 500 days post-infection

plasma pbmcs pbmc-derived 3-plex 13-plex 14-color
Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

PMID 41882353 · PMC13216075 · Nature · 2026 · 8 claims · 8 setups

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GluN1 and GluN2B NMDAR subunits are ectopically expressed in cancer cells of human TNBC tumours

breast tnbc 4t1-nmdar orthotopic bulk spatial immunofluorescence
Stage-specific epigenetic priming amplifies gene activation during lineage commitment.

PMID 41894493 · PMC13025117 · Science advances · 2026 · 8 claims · 8 setups

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Full-body Msl1 knockout causes embryonic lethality by E10.5, with morphological/developmental delay detectable already at E8.5

embryos e9.5 mesc-derived bright-field western 10x
Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.

PMID 41895287 · PMC13130636 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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12 weeks of vitamin D treatment decreases disease activity scores and inflammatory markers (fecal calprotectin) and improves quality of life in IBD patients

stool peripheral iga-bound ibd iga-seq igg-seq blood
scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

PMID 41907409 · PMC13019583 · iScience · 2026 · 8 claims · 8 setups

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scMILD identifies condition-associated cells using only sample-level labels via a dual-branch MIL architecture with a shared encoder

simulated lupus covid-19 ulcerative simulated mixture scrna-seq
Bisphenol a exposure and major depressive disorder: an integrative analysis combining network toxicology, molecular docking, genetic epidemiology, and transcriptomic validation.

PMID 41912493 · PMC13039830 · Translational psychiatry · 2026 · 8 claims · 8 setups

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571 shared targets identified between BPA-associated (2554) and MDD-associated (4661) genes

gene shared gwas gabaergic network ppi mendelian

Experiments

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

Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.

Single-cell transcriptome analysis reveals DNMT1(+) epithelial cells promote lymphatic metastasis via CXCL17-mediated TAM infiltration.

DAESC + : high-performance, integrated software for single-cell allele-specific expression data.

Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma.

Tumors located in the brain impair the frequency and phenotype of dendritic cells in blood and tumor.

Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis.

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea.

Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.

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

The macrophage entry mechanism of SARS-CoV-2 mediated by surface CD98/TMPRSS11E complex is associated with the cellular tropism toward proinflammatory M1 and pathogenesis.

OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

Dysregulated NK-cell gene expression defines the enduring symptoms of long COVID-19.

Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

Stage-specific epigenetic priming amplifies gene activation during lineage commitment.

Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.

scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

Bisphenol a exposure and major depressive disorder: an integrative analysis combining network toxicology, molecular docking, genetic epidemiology, and transcriptomic validation.