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).

• Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.

  PMID 41526189 · PMC12951969 · Genome research · 2026 · 8 claims · 6 setups

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  Early feature extraction (via ConvNeXt V2 blocks), rather than downstream architecture type, is the primary determinant of prediction accuracy in high-resolution chromatin accessibility prediction.

  lines cancer sets gm12878 atac-seq peak input-shift

• A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.

  PMID 41663439 · PMC12996591 · Nature communications · 2026 · 7 claims · 7 setups

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  Aggregating peaks from 624 high-quality bulk ATAC-seq datasets defines ~1.4 million observed consensus peaks (cPeaks) covering ~30% of the genome.

  bulk scatac-seq cnn gm12878 bulk scatac-seq deep

• isoSeQL: comparing long-read isoforms across multiple datasets.

  PMID 41452740 · PMC12790818 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  isoSeQL enables comparison of long-read isoform profiles across multiple datasets by consolidating SQANTI3-annotated samples into a unified SQLite database with consistent isoform IDs

  gencode simulated gm12878 peripheral intron simulated long-read

• 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