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).

• Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

  PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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  SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

  hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial

• scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

  PMID 41820391 · PMC13121454 · Nature communications · 2026 · 8 claims · 5 setups

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  scTWAS uses a latent-variable expression-measurement model combined with a moment-based regression to more accurately estimate genetic regulation of gene expression from single-cell data, improving GReX prediction across cell types and datasets

  onek1k-derived onek1k-based immune brain simulated two-sample stage

• scSurv: a deep generative model for single-cell survival analysis.

  PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

  simulated tcga melanoma renal scrna-seq bulk single-cell

• LIMPACAT: Multi-omics attention transformer for immune prediction in liver cancer using whole-slide imaging.

  PMID 41511965 · PMC12788640 · PloS one · 2026 · 8 claims · 6 setups

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  LIMPACAT, a multiple instance learning attention transformer, predicts immune cell levels relevant to HCC prognosis directly from whole-slide images

  hcc simulated pbmc tcga-lihc scrna-seq type deconvolution

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Prediction of myeloid malignant cells in Fanconi anemia using machine learning.

  PMID 41557613 · PMC12818649 · PloS one · 2026 · 6 claims · 7 setups

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  A DNN classifier trained on AML scRNA-seq data accurately predicts AML-like transcriptional profiles at single-cell resolution

  bone predicted-aml healthy scrna-seq reference-based stemnet

• Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer.

  PMID 41978385 · PMC13076935 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  scMnT identifies MSI cells and quantifies MSI intensity at single-cell resolution from scRNA-seq data using mononucleotide microsatellite allele length statistics

  crc cancer sc035 p20 scrna-seq snv msi

• Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

  PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

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  Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

  e18 pbmc brain kidney scrna-seq share-seq gas

• A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9(+) myeloid cells to drive type I interferon-driven inflammation in photosensitive autoimmunity.

  PMID 42032302 · PMC13226071 · Nature immunology · 2026 · 8 claims · 8 setups

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  MMP9+CD14+ myeloid cells are critical mediators of photosensitivity, expanding in lesional skin, producing IFNβ, and colocalizing with cytotoxic CD4+ T cells at the dermal-epidermal junction

  skin blister punch donor scrna-seq 250-plex seqfish

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• Immunosuppressive contribution of tumour-infiltrating B cells in human intrahepatic cholangiocarcinoma and their role in chemoimmunotherapy outcome.

  PMID 40889886 · PMC13217081 · Gut · 2026 · 8 claims · 7 setups

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  High density of CD20+ B cells in the peritumoural area is associated with improved disease-free survival in iCCA

  resected cd45+ scrna-seq peripheral immunohistochemistry kaplan-meier scrna-seq

• Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

  PMID 42058918 · PMC13123497 · iScience · 2026 · 7 claims · 6 setups

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  Fibroblast culture leads to subtype assimilation, with in vivo heterogeneity persisting only minimally by passage 4

  dermal mesenchymal stromal patient-matched single-cell bulk qpcr