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).

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

  PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 7 claims · 8 setups

  Has reproduction · 77

  PredTAD, a Gradient Boosting Machine model using epigenomic and genomic features plus neighboring-bin information, classifies 10 kb genomic regions as TAD boundary or non-boundary across normal and breast cancer cell lines.

  mcf10a t47d gm12878 mcf7 hi-c chip-seq atac-seq

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent