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).

• Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

  PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

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  GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

  breast anterior brain olfactory 10x starmap slide-seqv2

• SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

  PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

  gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish

• Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.

  PMID 41593733 · PMC12918531 · Genome biology · 2026 · 8 claims · 5 setups

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  Generated the first single-cell transcriptome atlas (scRNA-seq + spRNA-seq) of grapevine leaves during P. viticola infection across four early time points (0, 3, 6, 12 hpi)

  vitis guard cabernet tissue-specific single-cell spatial pseudo-time

• sCellST predicts single-cell gene expression from H& E images.

  PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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  sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

  ovarian kidney prostate breast simulation spot-level nucleus

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene