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).

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 4 setups

  Has reproduction · 67

  Removal of batch effects in reference scRNA-seq datasets (via Harmony-Symphony) benefits the task of cell composition deconvolution

  pbmc derived tcga-lihc scrna-seq simulated bulk

• Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

  PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 63

  Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

  hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

  Full-text index only

  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

  PMID 41540084 · PMC12894745 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  The presence of immune cells in the environment significantly alters CLL cell activation

  autologous monoculture non-adherent pbmc bulk flow deconvolution

• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

  PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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  FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

  colorectal crc breast he-stained spatial type ccc

• Alternative splicing dynamics during human cardiac development in vivo and in vitro.

  PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

  ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk

• Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

  PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Full-text index only

  Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

  pca tcga-prad external scrna-seq bulk immune

• Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy.

  PMID 41530481 · PMC12877007 · Scientific reports · 2026 · 7 claims · 8 setups

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  71 genes show concordant (same-direction) expression changes and 94 genes show concordant methylation changes across both the kindling and kainic acid epilepsy models

  hippocampus sequencing reduced-representation rt-pcr

• Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

  PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups

  Full-text index only

  446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways

  carotid degs six bulk kegg logistic

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential