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 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

• 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

• Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

  PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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  The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

  chimpanzee megablast pcr flanking-sequence

• Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

  PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

  metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• 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

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.

  PMID 19942684 · PMC2817474 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  Exogenous RPA4 expression does not support chromosomal DNA replication and causes cell-cycle arrest in G2/M

  hela mammalian rpa4 western flow immunofluorescence

• 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

• Continued colonization of the human genome by mitochondrial DNA.

  PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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  NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

  homo genomic chimpanzee genome genome-wide pcr sanger

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

  PMID 19682372 · PMC2735741 · BMC evolutionary biology · 2009 · 7 claims · 7 setups

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  Major NLRP genes duplicated before the divergence of mammals, with lineage-specific duplications in primates (NLRP7, NLRP11) and rodents (Nlrp1, Nlrp4, Nlrp9)

  mammalian cattle oocyte-expressed genome phylogenetic syntenic functional

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

  PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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  Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

  liver genomic tissues embryos rt-pcr genomic secondary

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• The meso-genomic era.

  PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups

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  Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).

  genome chromosome families tomato snp haplotype genetic

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger