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).

• 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

• SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.

  PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Has reproduction · 74

  SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.

  pairs nanostring st-sc osmfish_zeisel st-sc 5-fold spatially

• Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

  PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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  MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

  microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus

• Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

  PMID 41493197 · PMC13110159 · Plant biotechnology journal · 2026 · 8 claims · 5 setups

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  An optimised Visium spatial transcriptomics protocol (two-step OCT embedding combined with OCT-Immersion First cryopreservation) preserves high-integrity RNA from fragile plant tissues such as SAM

  maize integrated spatial integrity dimensional

• Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.

  PMID 41576947 · PMC12985369 · Cell genomics · 2026 · 7 claims · 7 setups

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  snRNA-seq census of 227,680 nuclei across 48 cell types reveals altered cellular states and compositional rewiring of the distal lung in ILD

  frozen lung flash-frozen spatial single-nucleus scrna-seq 10x

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed

• Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

  PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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  TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

  facs-sorted same integrated fgf9 hi-c chip-seq metaloci

• Single-cell spatial transcriptomic analysis of human skin anatomy.

  PMID 41872488 · PMC13083264 · Nature genetics · 2026 · 8 claims · 6 setups

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  MERFISH-based spatial atlas of ~1.2 million cells resolves 45 cell types across 114 samples and 15 anatomic sites in normal human skin

  normal skin gtex matched merfish scrna-seq bulk

• Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

  PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

  Has reproduction · 100

  S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

  gastric colorectal additional breast xenium visium histology

• A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.

  PMID 41518352 · PMC12790319 · European journal of immunology · 2026 · 8 claims · 5 setups

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  Imaging-based spatial transcriptomics (CosMx SMI) captures tissue complexity and cellular composition more faithfully than scRNA-seq

  palatine same tonsil cosmx imaging-based immunofluorescence scrna-seq

• Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

  PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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  MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

  lung ffpe lymph nonhuman scrna-seq spatial bulk

• Single nuclei and spatial profiling of sacrococcygeal teratomas reveals cellular composition and X inactivation heterogeneity.

  PMID 41565739 · PMC12949016 · NPJ precision oncology · 2026 · 7 claims · 4 setups

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  snRNA-seq and spatial transcriptomics of eight SCTs identify five broad cell lineages (neuroectoderm, epithelia, stroma, endothelia, immune) resolved into 26 transcriptionally distinct subtypes

  postnatal prenatal aggregated single-nucleus single-cell spatial

• DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

  PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

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  DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

  heart cortex visual brain spatial cell-type

• Spatiotemporal transcriptomic profiling reveals upregulation of glycolysis pathway genes before overt tauopathy in the PS19 mouse model.

  PMID 41688738 · PMC12992590 · Experimental & molecular medicine · 2026 · 7 claims · 7 setups

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  Pgk1, a glycolytic hub gene, is upregulated in the CA3 hippocampal subregion at 2 months of age, preceding detectable tau tangle pathology, and its expression correlates with tangle severity.

  ps19 spatial immunohistochemistry immunofluorescence

• 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

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.

  PMID 41507434 · PMC12891734 · Communications biology · 2026 · 8 claims · 6 setups

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  VISTA predicts unmeasured gene expression in subcellular spatial transcriptomic data by integrating scRNA-seq and SST through variational inference and geometric deep learning with built-in uncertainty quantification

  brain breast embryo muscle imaging-based sequencing spot-based

• BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

  PMID 17965094 · PMC2238987 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  BioHealthBase BRC is a public integrated bioinformatics database and analysis resource for influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin.

  avian pb2 dkxi35 ns1 sequence genome t-cell

• Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

  PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups

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  A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC

  pig lemur cv-1 b-prop1 bac comparative transient

• Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.

  PMID 41542331 · PMC12802566 · Health science reports · 2026 · 7 claims · 8 setups

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  BPC differentiation is significantly altered in UC, driven by a FABP1-led functional gene matrix

  colorectal colon patients bulk single-cell spatial bulk