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).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: k562 ✕ Assay: atac-seq ✕ Clear

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
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

PMID 41530870 · PMC12888741 · Genome medicine · 2026 · 8 claims · 8 setups

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MAAS integrates chromatin accessibility, CNVs, and SNVs from scATAC-seq data to identify functional tumor cell subpopulations

tumor pediatric b-cell glioblastoma scatac-seq bulk gene
Uncertainty-aware genomic deep learning with knowledge distillation.

PMID 41523993 · PMC12779563 · NPJ artificial intelligence · 2026 · 7 claims · 6 setups

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DEGU distills an ensemble of teacher DNNs into a single student model by jointly predicting the ensemble mean and the variability (epistemic uncertainty) across ensemble predictions.

drosophila k562 deepstarr starr-seq starr-seq-derived lentimpra base-resolution
CircleBase V2: an eccDNA annotation platform across cancers and species.

PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

raw eccdna tissues cancer circle-seq motif gene

Experiments

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

Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

Uncertainty-aware genomic deep learning with knowledge distillation.

CircleBase V2: an eccDNA annotation platform across cancers and species.