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: cell-type-specific ✕ Assay: h3k27ac ✕ Clear

EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

Full-text index only

EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

k562 lines likely cell-type-specific rna-seq cage abc
Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

Full-text index only

Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact
EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

Full-text index only

EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

dbps tfs common ctcf deep comparative feature-ablation
An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

PMID 41937210 · PMC13067603 · Genome biology · 2026 · 8 claims · 8 setups

Full-text index only

Constructed an integrated multiomic atlas of the human left ventricle combining ~2.3M snRNA-seq nuclei from 299 donors and ~690K snATAC-seq nuclei from 106 donors

left heart cardiac snrna-seq snatac-seq bulk

Experiments

EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.