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).
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Modeling nascent transcription from chromatin landscape and structure with CLASTER.
PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups
CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner
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Has reproduction · 90
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
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
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Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.
PMID 15907206 · PMC1156890 · BMC genomics · 2005 · 8 claims · 5 setups
Regulation of mRNA stability accounts for as much as 50% of all measured changes in polyA mRNA levels, inferred from absence of corresponding nuclear transcription changes.
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Has reproduction · 75
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.
PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups
A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.