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).

• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

  PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

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  scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

  pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

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  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.

  PMID 41555918 · PMC12812404 · Frontiers in genetics · 2025 · 7 claims · 5 setups

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  LiVAE, a dual-pathway VAE with Lorentzian geometric regularization between a primary Euclidean pathway and an information-bottleneck pathway, balances local fidelity with global topology coherence in single-cell embeddings

  single-cell same dapp1 benchmarking umap component-wise

• A ligand-centered framework for γδ T cell activation in colorectal cancer revealed by single-cell and transformer-based perturbation.

  PMID 41607803 · PMC12835328 · Frontiers in immunology · 2025 · 8 claims · 8 setups

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  CRC-infiltrating γδ T cells show varied activation levels, with the TRM-like population being the major tumor-infiltrating subtype and exhibiting the lowest effector and exhaustion signature scores.

  crc-infiltrating crc scrna-seq gene nichenet

• Comprehensive comparison of gene expression diversity among a variety of human stem cells.

  PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types

  escs stem batch-corrected degs bulk batch dimensionality