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).

• From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture.

  PMID 41507775 · PMC12870729 · BMC bioinformatics · 2026 · 8 claims · 3 setups

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  The 4DGBWorkflow and 4D Genome Browser (4DGB) are a containerized, cross-platform (macOS/Linux/Windows) toolkit that transforms Hi-C data into 3D chromosome reconstructions and provides comparative visualization

  a549 mus computationally hi-c molecular

• ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

  PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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  ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

  lines chromosome embryonic transcription chip-seq chromhmm hi-c