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 6

System / cell line: representative ✕ Assay: scrna-seq ✕ Clear

Benchmarking RNA velocity methods across 17 independent studies.

PMID 41916302 · PMC13106975 · Cell reports methods · 2026 · 8 claims · 6 setups

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No single RNA velocity method exhibited superior performance across all accuracy, stability, and usability assessments

scrna-seq same representative dyngen-simulated velocity cross-method downsampling
Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.

PMID 41942785 · PMC13053443 · Journal of molecular medicine (Berlin, Germany) · 2026 · 8 claims · 8 setups

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A PDAC-enriched myoCAF-c1 fibroblast cluster is closely associated with epithelial-mesenchymal transition (EMT) and angiogenesis

pdac myocaf-c1-derived tcga-paad scrna-seq spatial bulk
Community assessment of methods to deconvolve cellular composition from bulk gene expression.

PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups

Has reproduction · 63

Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.

admixtures cancer tumor bulk bulk admixture crowdsourced
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
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
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

Experiments

Benchmarking RNA velocity methods across 17 independent studies.

Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.

Community assessment of methods to deconvolve cellular composition from bulk gene expression.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

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

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