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).

• An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.

  PMID 15606920 · PMC544558 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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  SVD-based analysis of tetrapeptide frequency vectors can compare whole eukaryotic proteomes without pre-defining orthologs or aligning homologous sites

  predicted nine svd-derived ras svd species bootstrap

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

  PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

  Has reproduction · 58

  A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years

  cheetah lion genes methylation epigenome-wide differential

• Discordance of species trees with their most likely gene trees.

  PMID 16733550 · PMC1464820 · PLoS genetics · 2006 · 7 claims · 2 setups

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  For any species tree topology with n ≥ 5 taxa, there exist branch lengths for which the most likely gene tree topology (an 'anomalous gene tree') differs from the species tree topology.

  coalescent n-taxon analytical combinatorial

• Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

  PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

  synthetic eukaryotic simulated 16-species analytical comparative simulation

• 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

• Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

  PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

  eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• Species-specific protein sequence and fold optimizations.

  PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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  Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

  predicted mean over orf principal hierarchical domain-based

• Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

  PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

  metazoan identified amphimedon nematostella genome sequence gene

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 7 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across 4 cotton species (G. arboreum 20, G. raimondii 20, G. hirsutum 38, G. barbadense 36), clustering into 5 groups (I, II, III, IVa, IVb).

  plant cotton hirsutum ghcngc genome-wide phylogenetic conserved

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

  PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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  APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

  apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

  PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

  dart-possessing same land cantareus 28s shimodaira-hasegawa principal

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat