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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Systematic identification of pseudogenes through whole genome expression evidence profiling.
PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups
Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence
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Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups
Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods
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Sequence similarity network reveals common ancestry of multidomain proteins.
PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups
Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.
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Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.
PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups
Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins