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).

• Enteroendocrine cell lineages that differentially control feeding and gut motility.

  PMID 36810133 · PMC10032656 · eLife · 2023 · 6 claims · 8 setups

  Has reproduction · 88

  Vil1-p2a-FlpO knock-in mice combined with lineage-specific Cre lines enable highly selective intersectional genetic access to major enteroendocrine cell lineages (serotonin/enterochromaffin, GLP1, CCK, somatostatin, GIP) in vivo

  neurod1-cre neurog3-cre intestinal vil1-p2a-flpo single-cell fluorescence-activated two-color

• Interpretable and integrative analysis of single-cell multiomics with scMKL.

  PMID 40770488 · PMC12328712 · Communications biology · 2025 · 7 claims · 7 setups

  Has reproduction · 65

  scMKL outperforms SVM, EasyMKL, MLP, and XGBoost in classification accuracy (AUROC) across multiple single-cell cancer datasets

  mcf-7 t-47d small prostate 10x scrna-seq sciatac-seq

• Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.

  PMID 41786602 · PMC13138013 · Genome research · 2026 · 7 claims · 5 setups

  Full-text index only

  NNet uses PCA embedding followed by local KNN regression in PC space to construct cell-specific coexpression networks (CSNs), improving computational efficiency and estimate stability versus pairwise approaches.

  pbmc thp-1 lin small scrna-seq perturb-seq

• Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

  PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 7 setups

  Has reproduction · 37

  Orthogonal engineering with PD1d/IL-2v/IL-33 reprograms adoptively transferred CD8+ T cells into a novel synthetic effector state (C5/TSE) that deviates from canonical TOX+ exhaustion

  cd8+ b16-ova ot1 mice scrna-seq flow secretion

• Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.

  PMID 41501078 · PMC12780049 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  MAGPIE is a computational framework (Snakemake workflow) that co-registers Visium spatial transcriptomics with MSI metabolomics and tissue morphology images from same or consecutive sections

  lung brain publicly rodent spatial desi h&e

• Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.

  PMID 42206012 · PMC13202175 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups

  Full-text index only

  AVITI and NovaSeq X Plus are highly comparable overall for variant-calling performance in WGS

  tumor mm1s aviti chr20 whole-genome pacbio small

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome