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).

• The stem cell population of the human colon crypt: analysis via methylation patterns.

  PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

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  A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

  colon computational simulated bisulfite coalescent posterior

• Importance sampling for the infinite sites model.

  PMID 18976228 · PMC2832804 · Statistical applications in genetics and molecular biology · 2008 · 7 claims · 2 setups

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  A new importance sampling proposal distribution for the ISM, derived from a new result on exact sampling from a single segregating site, generally shows greater efficiency than the GT and SD proposals.

  simulated empirical computational reanalysis

• Computation of haplotypes on SNPs subsets: advantage of the "global method".

  PMID 17067372 · PMC1636337 · BMC genetics · 2006 · 6 claims · 4 setups

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  The global method for subhaplotyping always yields a lower error rate than the direct method across datasets and SNP subset sizes

  gh1 apoe coalescent-model-simulated griv computational genetic

• Direct maximum parsimony phylogeny reconstruction from genotype data.

  PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

  simulated mitochondrial lipoprotein coalescent maximum sliding-window

• Sex-biased evolutionary forces shape genomic patterns of human diversity.

  PMID 18818765 · PMC2538571 · PLoS genetics · 2008 · 7 claims · 5 setups

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  X-linked diversity is higher than the neutral expectation (0.75) relative to autosomal diversity in all six sampled human populations

  humans population simulated computational resequencing coalescent-based coalescent