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).

• 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

• Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

  PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

  skin combined annotated scrna-seq single-cell spatial cell2location

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 90

  Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

  sural peripheral snrna-seq nerve single-nucleus subcellular situ

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 8 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific transcriptome signatures in cord blood, with a significant sex-by-exposure interaction for many genes.

  cord maternal pm2.5-associated blood whole-genome spatial-temporal overrepresentation

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta.

  PMID 37196086 · PMC11809670 · Science advances · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  CAMAs are located in the epidermis of the tentacle tips of P. acuta polyps

  pocillopora acuta lcm-isolated whole-mount fish transmission

• 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

• Comparative single-cell landscape of immune cells in human livers affected HBV and non-viral cirrhosis.

  PMID 41815278 · PMC12971635 · Frontiers in medicine · 2025 · 8 claims · 7 setups

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  Macrophage-PLCG2 (anti-inflammatory) and CD8+ T-FABP5 subsets are expanded in HBV cirrhosis compared to non-viral cirrhosis

  liver myeloid scrna-seq spatial pathway

• Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression.

  PMID 33722289 · PMC7962346 · Genome biology · 2021 · 7 claims · 8 setups

  Has reproduction · 66

  A three-base-pair (HDR) or single-base (PE2) substitution in the Tspan2 CArG box causes cell-specific loss of Tspan2 mRNA in aorta and bladder, but not heart or brain

  tissues zygotes aorta spleen qrt-pcr allele-specific restriction

• Investigating the genetic association between ERAP1 and ankylosing spondylitis.

  PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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  The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

  patients cases genotype comparison snp meta-analysis resequencing

• Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.

  PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups

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  PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit

  tumor paired single-cell bulk multiplex

• Global reorganization of genome architecture at the transition to gametogenesis.

  PMID 41721019 · PMC12999497 · Nature structural & molecular biology · 2026 · 8 claims · 8 setups

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  Premeiotic gonadal germ cells display a distinct chromosome and genome architecture concomitant with commitment to gametogenesis, involving separation of individual chromosomes, peripheral centromere anchoring, reduced interchromosomal interactions and disentangled chromosome ends

  e13.5 e9.5 gonadal facs-sorted transmission immunofluorescence minor

• Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.

  PMID 41776501 · PMC13162433 · Molecular cancer · 2026 · 8 claims · 6 setups

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  MeRLin, a single-vector high-complexity lineage tracing platform integrating cellular barcoding, scRNA-seq, RNA-FISH, and computational analysis, was developed to track clonal and transcriptional dynamics in a melanoma PDX model

  wm4237-1 nsg bulk scrna-seq clonal

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• 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

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  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