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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A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.
PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups
Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)
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A statistical approach for array CGH data analysis.
PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups
Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data
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Simple models of genomic variation in human SNP density.
PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups
Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.
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Duplication count distributions in DNA sequences.
PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups
Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.