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).

• Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

  PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

  cd4+ computational hep direct simulation epigraph

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• DNA demethylation is associated with malignant progression of lower-grade gliomas.

  PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

  gliomas neural analysis tcga methylation whole-exome sequencing

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

  PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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  CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

  neuroblastoma nlf athymic methylation-specific quantitative soft

• Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.

  PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 83

  Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD

  tcga gse13213 gse31210 multiomics closest ssgsea

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 7 claims · 8 setups

  Has reproduction · 80

  DME-mediated nicking enables DMN-seq (DMN+) to detect 5mC at single-base resolution by ligating adaptors only to 5mC-containing fragments generated by DME excision

  synthetic partially embryonic mesc dmn+ ubs-seq dmn–

• The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

  PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

  Full-text index only

  GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

  polish cohort nonsmokers low genome-wide biomarker epidemiological

• A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

  PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

  Has reproduction · 91

  DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.

  solid muscle-invasive ccrcc for bulk single-cell scrna-seq