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).

• The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.

  PMID 41978268 · PMC13076225 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Single-nucleus Hi-C reveals CTCF-independent contact domains with stable boundaries defined by convergently oriented transcription units (TUs)

  chicken computational oocytes single-nucleus nome-seq rna-seq

• Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution.

  PMID 41980945 · PMC13250166 · Nature communications · 2026 · 8 claims · 8 setups

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  Hi-Compass predicts cell-type-specific Hi-C contact maps using only ATAC-seq as cell-type-specific input, plus DNA sequence and a generalized CTCF binding profile

  gm12878 curated bulk training hi-c ctcf matched

• Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data.

  PMID 41633996 · PMC12976324 · Nature communications · 2026 · 8 claims · 8 setups

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  ICE and KR matrix balancing normalization methods over-correct and attenuate low-frequency enhancer-promoter loop signals despite preserving structural (CTCF-mediated) loops

  gm12878 embryonic mescs hi-c chip-seq chia-pet

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray