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).

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated

• 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

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  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• Bayesian coestimation of phylogeny and sequence alignment.

  PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

  globin same four-sequence bayesian mcmc comparison

• EGenBio: a data management system for evolutionary genomics and biodiversity.

  PMID 17118150 · PMC1683573 · BMC bioinformatics · 2006 · 7 claims · 7 setups

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  EGenBio is a web-based system for integrated management, filtering, curation, and visualization of large-scale genomic sequences, alignments, and phylogenetic trees for evolutionary genomics and biodiversity research.

  vertebrate sequence mutant phylogenetic sequence coevolution saturation

• Bayesian estimates of linkage disequilibrium.

  PMID 17592642 · PMC1924864 · BMC genetics · 2007 · 8 claims · 3 setups

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  The MLE of D' is biased toward disequilibrium, with the bias particularly severe in small samples (<100 subjects) and rare alleles (MAF<0.05)

  simulated genotype pairwise computer genotype bayesian

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon