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).

• CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference.

  PMID 42059479 · PMC13130071 · Briefings in bioinformatics · 2026 · 7 claims · 5 setups

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  CaHoT-GRN integrates pretrained biological language model embeddings (DNABERT for DNA, ESM for protein) with scRNA-seq expression data to improve GRN inference

  embryonic gene dataset-specific same scrna-seq-based sequence protein-protein

• GRNFormer: accurate gene regulatory network inference using graph transformer.

  PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

  hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string

• A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

  PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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  MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

  skin blister punch donor scrna-seq 250-plex seqfish

• singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.

  PMID 41838773 · PMC13008255 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  singIST provides explainable quantitative measures of disease model similarity to a human reference at the pathway, cell type, and gene levels

  skin ear simulated scrna-seq simulation

• 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