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 single-cell multiomics reveals peripheral immune dysfunction in Parkinson's and inflammatory bowel disease.

  PMID 41545356 · PMC12847817 · NPJ Parkinson's disease · 2026 · 8 claims · 5 setups

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  Spatial single-cell multiomic imaging of sigmoid colon reveals both shared and unique features of peripheral immune dysfunction in PD and IBD

  sigmoid plasma stool epithelial cosmx meso gene

• Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.

  PMID 41895287 · PMC13130636 · Cell reports. Medicine · 2026 · 8 claims · 7 setups

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  12 weeks of vitamin D treatment decreases disease activity scores and inflammatory markers (fecal calprotectin) and improves quality of life in IBD patients

  stool peripheral iga-bound ibd iga-seq igg-seq blood

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

  PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

  consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene

• Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

  PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups

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  CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC

  intestinal colorectal single-cell serum bulk single-cell spatial

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 7 claims · 6 setups

  Has reproduction · 65

  UC patient-derived organoids histologically phenocopy primary UC tissue, showing disorganized stratified epithelium, reduced mucin/goblet cells, and non-uniform proliferation compared to non-IBD organoids

  patient-derived h3k27ac rna-seq chip-seq histology

• Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

  PMID 37563310 · PMC10457199 · Nature immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  Genome-wide pQTL mapping of 91 inflammation-related plasma proteins in 14,824 participants identified 180 significant pQTLs (59 cis, 121 trans) across 108 genomic regions and 70 proteins

  plasma blood tissues gut genome-wide pqtl cis-eqtl

• Multi-omics feature engineering driven by biomedical foundation models improves drug response prediction for inflammatory bowel disease patients.

  PMID 41844950 · PMC13129071 · Scientific reports · 2026 · 8 claims · 7 setups

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  FM (MAMMAL)-derived drug-target binding affinity (BA) inference can be used to rank/select biologically relevant protein targets and their associated genes/SNPs for a drug of interest without knowledge of protein structure or active sites

  reference top surgical snp-mutated inference gene genomic

• Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution.

  PMID 41513700 · PMC12891662 · Nature communications · 2026 · 8 claims · 8 setups

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  Cytomix (TNFɑ+IFNɣ+IL1β) treatment of human colon organoids best recapitulates molecular features of human IBD compared to DSS or irradiation injury models.

  colon cytomix-treated scrna-seq immunofluorescence activated