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).

• Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

  PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

  Has reproduction

  Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

  types encode chip-seq chromhmm dnase-seq

• JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

  PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

  encode genes invertebrate initio comparative training

• Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

  PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

  Full-text index only

  A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

  bidirectional across high-quality nascent comparative eqtl

• GeMI: interactive interface for transformer-based Genomic Metadata Integration.

  PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups

  Has reproduction · 64

  GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.

  cistrome encode geo fine-tuned manual batch transformer-based

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

  Full-text index only

  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see