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).

• An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.

  PMID 41922356 · PMC13212934 · Nature communications · 2026 · 8 claims · 7 setups

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  BioSeq2Seq is a transformer-based deep learning framework that predicts genome-wide transcriptional regulatory profiles at 128-bp resolution by jointly using RO-seq data and DNA sequence as tri-modal input

  k562 gm12878 imr-90 ro-seq chip-seq functional

• Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.

  PMID 42258536 · PMC13244158 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RADIAnT is a reads-to-interactions computational pipeline for analyzing RNA–DNA ligation data

  embryonic k562 mesc endothelial grid-seq radicl-seq red-c

• Long non-coding RNA LINC00607 epigenetically regulates endothelial TSPAN18 to promote hypoxia-induced thromboinflammation.

  PMID 41581880 · PMC12992942 · The Journal of biological chemistry · 2026 · 8 claims · 8 setups

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  LINC00607 is a hypoxia-inducible, endothelial-enriched lncRNA that positively regulates TSPAN18 expression

  huvecs rna-seq gro-seq atac-seq