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).

• CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

  PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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  CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

  species gm12878 types chromatin cross-protein cross-cell-type

• Modeling nascent transcription from chromatin landscape and structure with CLASTER.

  PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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  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

  embryonic mescs chromatin k562 eu-seq chip-seq micro-c

• Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.

  PMID 41688823 · PMC12904797 · Nature cell biology · 2026 · 8 claims · 8 setups

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  IDR function depends on two distinct but related properties: sequence specificity (motifs) and chemical specificity (distributed multivalent chemistry)

  cerevisiae orthologous abf1 fus1-163 plasmid anti-flag proteome-wide

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm