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).

• 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

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.

  mammary aggregated single-cell quality doublet

• Protocol for single-cell optimization objective and trade-off inference.

  PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups

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  SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs

  mcf10a serum-starved contact-inhibited zygote bulk scrna-seq genome-scale

• Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.

  PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.

  luad tcga cd8+ degs single-cell cibersort survival

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

  PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

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  MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

  bulk single-cell tcga glioma gsva aucell machine