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).
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Inparanoid: a comprehensive database of eukaryotic orthologs.
PMID 15608241 · PMC540061 · Nucleic acids research · 2005 · 8 claims · 4 setups
The Inparanoid algorithm identifies true ortholog clusters by seeding on reciprocal best-matching pairs, gathering inparalogs (post-speciation duplicates) while excluding outparalogs (pre-speciation duplicates)
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Reconstruction of human protein interolog network using evolutionary conserved network.
PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups
A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.
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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups
InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.
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Designating eukaryotic orthology via processed transcription units.
PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups
Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs