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).

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• 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

• Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

  PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

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  Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

  disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• Comparative analysis of cancer genes in the human and chimpanzee genomes.

  PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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  All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

  chimpanzee non-human cancer comparative pcr targeted

• 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

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• 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

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• Getting positive about selection.

  PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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  Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

  genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood

• Heterotachy in mammalian promoter evolution.

  PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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  The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

  promoter ancient chimpanzee comparative ancient micro-indel