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).

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip.

  PMID 17894875 · PMC2211321 · BMC genomics · 2007 · 8 claims · 6 setups

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  Efficiency of sequence recovery and accuracy of SNP identification on a species-specific resequencing microarray decline as sequence divergence from the reference increases.

  mtdna chimpanzee gorilla atlantic resequencing dideoxy phylogenetic

• 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

• 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

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• 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

• Inconsistencies in Neanderthal genomic DNA sequences.

  PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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  The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

  neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic