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).

• Identification and analysis of co-occurrence networks with NetCutter.

  PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

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  Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

  publime bipartite randomized co-occurrence null-model signal-to-noise

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

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  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac