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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Polymorphix: a sequence polymorphism database.
PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups
Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.
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Gene duplication: the genomic trade in spare parts.
PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups
Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.
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Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.
PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups
A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.
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Coverage of whole proteome by structural genomics observed through protein homology modeling database.
PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups
FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.