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

  Full-text index only

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

  simulated hypothalamus dorsolateral spatial clustering cell-cell

• SpaJoint: a transfer learning method for spatial transcriptomics deconvolution.

  PMID 41955028 · PMC13069903 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

  Full-text index only

  SpaJoint is a transfer-learning-based deconvolution method that integrates scRNA-seq and ST gene expression while accounting for spatial correlation across spots.

  simulated 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

  Full-text index only

  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

• SA2E: spatial-aware auto-encoder for cell type deconvolution of spatial transcriptomics data.

  PMID 41863296 · PMC13070677 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  SA2E is a spatial-aware auto-encoder framework for cell-type deconvolution that does not require predefined cell-type biomarkers

  olfactory legacy breast brain simulated real scrna-seq

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

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

  Full-text index only

  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

• SMART: spatial multi-omic aggregation using graph neural networks and metric learning.

  PMID 41896208 · PMC13031631 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  SMART accurately identifies spatial regions of anatomical structures and is compatible with spatial datasets of any type and number of omics layers

  simulated lymph brain spleen simulated spatial multi-section

• Heterozygous ADAR mutant mice exhibit RNA sensing-dependent neuroinflammation and phenotypes associated with Aicardi-Goutières syndrome.

  PMID 41704749 · PMC12907846 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  A heterozygous Adar G1007R (mouse G956R/G567) mouse model recapitulates the genetic and inflammatory features of human ADAR G1007R AGS patients

  brain computational coronal adar1 real-time bulk ingenuity

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

  Full-text index only

  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• Ex Vivo Immuno-Oncology Platform Reveals Spatial T-cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer.

  PMID 41563843 · PMC7618831 · Cancer immunology research · 2026 · 8 claims · 8 setups

  Full-text index only

  iPDCs cultured on human omentum gel (OmGel) recapitulate tumor genomic and histologic characteristics while retaining intratumoral immune cells

  formalin-fixed blood dissociated ipdcs histopathology whole-exome flow

• PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.

  PMID 41673899 · PMC12998178 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  PreTSA dramatically reduces computational time and memory versus GAM (Monocle, TSCAN) and PseudotimeDE for identifying temporally variable genes (TVGs) while producing highly similar results

  simulated null pbmc pancreas pseudotime tvg false-positive

• HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

  PMID 41764165 · PMC13065825 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  HRCHY-CytoCommunity is an end-to-end graph neural network framework that jointly identifies multi-level (coarse tissue compartment and fine cellular neighborhood) tissue structures from cell-type spatial maps using differentiable graph pooling, adaptive edge pruning, and consistency/balance regularization.

  healthy colorectal simulated breast codex visium merfish

• Cell neighborhood topology directs rare cell population identification.

  PMID 41912521 · PMC13199379 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  RareQ is a framework that quantifies neighborhood connectivity (Q), a cell-specific measure of kNN-graph cliquishness, to detect rare cell populations from single-cell and spatial omics data

  downsampled pbmc brain simulated scrna-seq cite-seq single-cell

• Point mutations in GLI3 lead to misregulation of its subcellular localization.

  PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

  Full-text index only

  The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

  hela immunofluorescence real-time luciferase

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

  Full-text index only

  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman

• Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

  PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

  Full-text index only

  Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

  neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• Direct inference of SNP heterozygosity rates and resolution of LOH detection.

  PMID 18052545 · PMC2098867 · PLoS computational biology · 2007 · 6 claims · 7 setups

  Full-text index only

  A large proportion of SNPs in dbSNP have high-variance HET rate estimates, limiting their reliability for LOH study design.

  dbsnp theoretical simulated hapmap snp probability sequential

• A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

  PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

  crc epithelial rcrc tcga-read scrna-seq copy gene