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).

• Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

  PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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  High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

  canine osteosarcoma independent third oligonucleotide cross-species quantitative

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional

• 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

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• 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

• Ecotype diversity and conversion in Photobacterium profundum strains.

  PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

  photobacterium profundum predicted orthologous whole-genome pulsed-field comparative

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco