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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Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.
PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups
GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.
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Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.
PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups
Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.
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Discovery and hypothesis generation through bioinformatics.
PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups
Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data
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SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups
SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models