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).

• SpliceHarmonization: an integrated method for identifying RNA splicing events in therapeutics for splicing modulation.

  PMID 41858229 · PMC13064980 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  SpliceHarmonization integrates rMATS, LeafCutter, and MAJIQ outputs into a unified junction-centered format with standardized event type annotations via event graph construction

  sma simulated bulk splicing rt-pcr

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

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  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• CAF-enriched COL4A6 promotes gastric cancer progression and stromal remodeling despite an inverse association in bulk transcriptomes.

  PMID 41735371 · PMC13031391 · Scientific reports · 2026 · 7 claims · 7 setups

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  COL4A6 carries an inverse association (OR<1) in bulk transcriptome-based risk models despite being markedly upregulated and predominantly localized to the CAF compartment in clinical specimens

  tcga-stad gse66229 gse183904 paired bulk microarray scrna-seq

• Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.

  PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)

  ipf degs differentially bleomycin-induced bulk methylation kegg

• DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.

  PMID 41707654 · PMC12923980 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  DeCAF is a single-sample kTSP classifier using 9 TSP gene pairs that predicts proCAF vs restCAF subtypes from bulk expression data

  pdac cptac external elyada-sc bulk single-sample classifier

• Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

  PMID 41562071 · PMC12813044 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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  GDPD3 is upregulated in PRAD tumor tissue and its knockdown inhibits tumor cell proliferation, invasion, and migration

  prad tcga-prad du145 scrna-seq bulk wgcna

• Epigenetic context defines the transcriptional activity of canonical and noncanonical NF-κB signaling in pancreatic cancer.

  PMID 41844578 · PMC13039881 · Cell death discovery · 2026 · 8 claims · 8 setups

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  TNFα is the primary activator of canonical NF-κB signaling via RELA in PDAC

  pdac patient-derived aspc-1 l3.6pl single-cell bulk multiplex

• Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

  PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

  Has reproduction · 83

  AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

  stage patients tumour whole-tumour radiomics bulk cellular

• Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

  PMID 41484106 · PMC12881549 · Nature communications · 2026 · 8 claims · 8 setups

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  Loss/inhibition of IKKα unexpectedly promotes, rather than suppresses, CRC liver metastasis in patient-derived organoid (PDO) xenograft models.

  pdo5 pdo5-derived crc dld1 intrasplenic immunohistochemistry kaplan-meier

• Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

  PMID 41419303 · PMC13151493 · Gut · 2026 · 8 claims · 8 setups

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  KC-Cpa1 mice show markedly increased pancreatic remodelling, fibrosis and metaplastic/PanIN lesion formation compared with KC mice

  pancreas cre acinar scrna-seq histology bulk single-cell

• Aging-associated differences in mammary tumor-initiating populations and immune evasion pathways in breast cancer.

  PMID 41719331 · PMC12933083 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  Age at NMU exposure critically influences tumor incidence, mutational burden, molecular subtype, and the tumor immune microenvironment

  virgin mammary tcga-brca carcinogen-induced immunofluorescence bulk

• Lipid droplet-mediated macrophage reprogramming drives fibroblast activation in keloid-associated inflammation.

  PMID 41840659 · PMC13063924 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  Keloid-associated macrophages (KAM) and skin-associated macrophages (SAM) represent transcriptionally distinct populations, with KAM showing enhanced lipid metabolism and M2/pro-fibrotic signatures

  skin keloid pbmc-derived macrophages single-cell immunofluorescence macrophage-sebocyte

• Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor.

  PMID 41931622 · PMC13048245 · Science advances · 2026 · 7 claims · 8 setups

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  Brain-specific (neural crest-derived, NC-SMC) but not peripheral (LPM-SMC/PM-SMC) iPSC-derived VSMCs are selectively vulnerable to CADASIL NOTCH3 variants

  ipsc-derived ivsmcs immunofluorescence wound collagen

• The Aging Microenvironment Is a Determinant of Immune Exclusion and Metastatic Fate in Pancreatic Cancer.

  PMID 41202211 · PMC12768431 · Cancer research · 2026 · 8 claims · 8 setups

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  Organismal aging accelerates PDAC progression and metastatic burden in an age-relevant syngeneic orthotopic mouse model

  kpc4662 orthotopic pdac pancreatic orthotopic heterochronic ultrasound