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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CGHPRO -- a comprehensive data analysis tool for array CGH.
PMID 15807904 · PMC1274268 · BMC bioinformatics · 2005 · 8 claims · 3 setups
CGHPRO is a user-friendly, versatile, stand-alone Java tool for normalization, visualization, breakpoint detection and comparative analysis of array-CGH data
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Has reproduction · 71
Spatial organization shapes the turnover of a bacterial transcriptome.
PMID 27198188 · PMC4874777 · eLife · 2016 · 7 claims · 6 setups
The E. coli transcriptome is spatially organized genome-wide: mRNAs encoding inner-membrane proteins are enriched at the membrane, while mRNAs encoding cytoplasmic, periplasmic and outer-membrane proteins are distributed throughout the cytoplasm.
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QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.
PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups
QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)