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).

• Charting spatial ligand-target activity using Renoir.

  PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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  Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

  intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell

• Characterizing gene perturbations in single cells via network divergence analysis.

  PMID 41965857 · PMC13249949 · Nature communications · 2026 · 8 claims · 8 setups

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  scDNS quantifies gene-specific functional perturbations by measuring Jensen-Shannon divergence between condition-specific gene interaction network configurations

  ipsc-derived embryonic panc-1 triple scrna-seq single-nucleus

• Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.

  PMID 41984780 · PMC13082667 · PLoS computational biology · 2026 · 7 claims · 4 setups

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  IGNITE is an unsupervised framework that infers directed, weighted, and signed GRNs directly from unperturbed scRNA-seq data using the inverse problem for a kinetic Ising model.

  pluripotent scrna-seq gene perturbation

• Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.

  PMID 40811813 · PMC12830129 · Blood advances · 2026 · 6 claims · 8 setups

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  Bex1 (and to a lesser extent Bex4) is ectopically expressed in Pten-deficient mouse T-ALL blasts

  thymocytes thymocyte t-all normal scrna-seq rt-qpcr bulk

• GAMMI: graph-guided contrastive and adversarial integration of single-cell and spatial multi-omics data.

  PMID 42108634 · PMC13158126 · Briefings in bioinformatics · 2026 · 6 claims · 5 setups

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  GAMMI consistently outperforms state-of-the-art integration methods (GLUE, Harmony, MIDAS, scMoMaT) in biological conservation and batch correction across five mosaic single-cell multi-omics benchmarks

  pbmc postmortem gse138852 gammi-derived multi-omics scrna-seq differential

• Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.

  PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 8 claims · 8 setups

  Has reproduction

  A 12-step CTC-specific scRNA-seq workflow is proposed, spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis, to overcome methodological inconsistencies in the field.

  ctcs pooled single neuroblastoma scrna-seq multi-omics

• Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development in vivo

  ugm hi-myc prostate hmyctg+ genetically single-cell immunohistochemistry

• 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