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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Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.
PMID 17127215 · PMC5054070 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 4 setups
Incorporating more sequence evolution features (transition/transversion bias, nucleotide/codon frequency bias) into Ka/Ks estimation methods yields more accurate and reliable estimates.
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Computing Ka and Ks with a consideration of unequal transitional substitutions.
PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups
MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias
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Nucleosome deposition and DNA methylation at coding region boundaries.
PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups
Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.
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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.