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).

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• Periodicity of SNP distribution around transcription start sites.

  PMID 16579865 · PMC1448210 · BMC genomics · 2006 · 8 claims · 6 setups

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  SNP density around TSS shows a 146-nucleotide periodicity

  genome human-chimpanzee tss promoter snp sequence cpg

• Patterns and rates of intron divergence between humans and chimpanzees.

  PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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  Intron divergence (Ki) is strongly positively correlated with intron length

  orthologous genome whole-genome cpg recombination

• Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

  PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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  Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

  autosomal intronic chimpanzee genes comparative human-chimpanzee background

• Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

  PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

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  CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

  randomly real human-chimpanzee simulated simulation comparative

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• A macaque's-eye view of human insertions and deletions: differences in mechanisms.

  PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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  Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

  chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis