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

• 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

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Imputation-based analysis of association studies: candidate regions and quantitative traits.

  PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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  Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

  study phenotyped genotype bayesian

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

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  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc