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).

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  Disease-specific temporal (dynamic) gene expression and splicing signatures, distinct from fixed timepoint differential expression, can be derived from DSS and adoptive transfer colitis models to capture acute-chronic disease dynamics

  colon blood distal ibd bulk qpcr histopathology

• Impact of enteric neuronal loss on intestinal cell composition.

  PMID 42063560 · PMC13127327 · iScience · 2026 · 8 claims · 7 setups

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  ENS loss in ret mutant zebrafish alters the non-neuronal composition of the intestine, with increased immune cells and shifts in epithelial and ECM-producing populations

  intestine ens immune phox2bb single-cell scrna-seq whole-mount

• Secreted phospholipase PLA2G5 acts as a hemolytic factor in sepsis.

  PMID 42065235 · PMC13132393 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  Pla2g5 gene expression is induced in the colon and small intestine during LPS-induced endotoxemia and CLP-induced sepsis in mice

  colon mice serum bone whole-mount rna-seq survival

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

  PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  stDyer-image directly associates the image modality with predicted cluster labels rather than using images to enhance/impute gene expression data

  non-small morphology brain breast spatial image

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.

  PMID 42116832 · PMC13157608 · Wellcome open research · 2026 · 7 claims · 8 setups

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  Aurelia sp. 4 chromosomal genome assembly has a total length of 462.10 Mb with 99.99% of sequence scaffolded into 21 chromosomal pseudomolecules

  aurelia microbial pacbio hi-c rna-seq

• Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

  PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

  aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr