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).

• 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

• 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

• Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

  PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

  same genes orangutan codeml gene sequence

• Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.

  PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple

  japonica arabidopsis pigment bulk functional

• Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

  PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  Assembled the first chromosome-level genome of G. vermiculophylla: 77.5 Mb, 22 pseudochromosomes, contig N50 2.61 Mb, scaffold N50 3.16 Mb

  vermiculophylla assembled predicted genome short-read nanopore hi-c

• 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

• 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