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).

• Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.

  PMID 42024616 · PMC13188987 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  MUSTARD is a trajectory-guided dimensionality reduction method for multi-sample, multi-condition scRNA-seq data that simultaneously captures gene expression variation along pseudotime and across samples

  simulated covid-su covid-stephenson tuberculosis data-driven scrna-seq pseudobulk-pca

• Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.

  PMID 41895263 · PMC13106970 · Cell reports methods · 2026 · 8 claims · 5 setups

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  scRNA-seq references yield significantly higher Pearson correlation and lower RMSE than snRNA-seq references for deconvolution across all four tissue datasets

  adipose same fat-cell real pseudobulk single-cell synthetic

• Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

  PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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  EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

  crc epcam+ aggregated cancer scrna-seq copy pseudobulk

• Ion-Channel-Mediated Drug Repurposing Opportunities Validated by Single-Cell Perturbation in Colorectal Cancer.

  PMID 42074061 · PMC13116841 · International journal of molecular sciences · 2026 · 8 claims · 6 setups

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  WGCNA on CRC transcriptomes identified 100 hub genes spanning three functional programs: ribosomal biogenesis, RNA processing, and immune

  crc independent hct116 bulk protein-protein vgae-based

• Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

  PMID 42025535 · PMC13105851 · Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026 · 8 claims · 8 setups

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  A pediatric single-cell PBMC reference atlas was developed from 57 healthy children across 8 public scRNA-seq studies.

  pbmcs cd3+ cd4+ memory scrna-seq pseudobulk bulk