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

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• How negative sampling shapes the performance of transcription factor binding site prediction models.

  PMID 41601205 · PMC12910371 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups

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  Negative sampling technique significantly impacts TFBS prediction model performance and interpretation of results

  encode same genome chip-seq atac-seq deep

• 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

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  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

• pmid-41728950

  PMID 41728950 · PMC12926921 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

  PMID 41882679 · PMC13019944 · Genome biology · 2026 · 8 claims · 7 setups

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  The majority of long-range intronic RNA duplexes detected genome-wide are mediated by inverted Alu-repeat elements.

  k562 hek293t chimpanzee computational splash eclip-seq