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).

• scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

  PMID 41877186 · PMC13134144 · Genome biology · 2026 · 8 claims · 7 setups

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  scComm infers cell-cell communications at single-cell resolution using a data-adaptive L-R weighting module and supervised contrastive learning (SupCon loss) to distinguish significant CCC events from background noise

  simulated spatial liver single-cell simulated spatial scrna-seq

• Spider: a flexible and unified framework for simulating spatial transcriptomics data.

  PMID 41237053 · PMC12790819 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  Spider simulates ST data without requiring real ST data as a reference

  simulated hypothalamus dorsolateral spatial clustering cell-cell

• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

  PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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  FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

  colorectal crc breast he-stained spatial type ccc

• RESCUE: recovery of unattributed expression patterns in spatial transcriptomics.

  PMID 41963343 · PMC13247165 · Nature communications · 2026 · 8 claims · 5 setups

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  Existing ST analysis methods (segmentation, deconvolution) systematically omit or mislabel a substantial portion of true molecular expression

  synthetic honey simulation merfish segmentation