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).

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

  PMID 19789336 · PMC2927135 · Cancer research · 2009 · 8 claims · 8 setups

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  K-RAS and N-RAS mutation status differentially determine the level of TNFα-induced apoptosis in an isogenic colon carcinoma cell panel

  isogenic same conditioned dld-1 flow luminex immunoblot

• Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

  PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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  A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

  larc scrna-seq scissor+ single-cell bulk pseudotime

• 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

• Single-cell sequencing analysis and machine learning model reveal aberrant TIM-3 expression in microglia during Alzheimer's disease progression.

  PMID 41580850 · PMC12911240 · Journal of translational medicine · 2026 · 7 claims · 8 setups

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  A TIM-3+ microglial subset drives AD pathogenesis through a dual mechanism: sustained neuroinflammation via TNF-α/NF-κB and IL-6/JAK/STAT3 signaling, and impaired amyloid-β clearance linked to PI3K-AKT and FcγR pathways

  brain overlapping transcriptomic patients single-cell bulk kegg

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

  PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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  OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

  tcga-luad geo lung single-cell bulk ssgsea cibersort

• SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

  PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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  SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

  prostate gwas eqtl bph single-cell mendelian bayesian

• Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.

  PMID 41732268 · PMC12925236 · iScience · 2026 · 8 claims · 8 setups

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  Two severity-associated classical monocyte (cMono) subtypes, IL7R+ and CD163+, exist with distinct transcriptional and epigenetic landscapes.

  pbmcs pbmc classical cmono single-nucleus differential multimodal

• Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

  PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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  The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

  tcga-brca senescent normal single-cell machine univariate gene

• Comprehensive immune profiling reveals IFN-γ signaling in T cells mediates parasite phagocytosis in a rodent malaria model.

  PMID 41810957 · PMC13059739 · mBio · 2026 · 8 claims · 8 setups

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  IFN-γ signaling in T cells contributes to the development of malaria-associated lung pathology

  lungs pbnk65-infected cell-specific lung flow time-series qrt-pcr

• Comparative single-cell landscape of immune cells in human livers affected HBV and non-viral cirrhosis.

  PMID 41815278 · PMC12971635 · Frontiers in medicine · 2025 · 8 claims · 7 setups

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  Macrophage-PLCG2 (anti-inflammatory) and CD8+ T-FABP5 subsets are expanded in HBV cirrhosis compared to non-viral cirrhosis

  liver myeloid scrna-seq spatial pathway