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).

Publications 1.3k Datasets 392.5k Experiments 125

System / cell line: species ✕ Assay: phylogenetic ✕ Clear

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

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

Full-text index only

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
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic
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

Full-text index only

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
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

Full-text index only

The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups

Full-text index only

hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)

multi-species recombinant immunoprecipitated hela phylogenetic gtp gtpase
Helminth genomics: The implications for human health.

PMID 19855829 · PMC2757907 · PLoS neglected tropical diseases · 2009 · 8 claims · 7 setups

Full-text index only

More than two billion people (one-third of humanity) are infected with helminth parasites, causing major morbidity, mortality, and poverty maintenance

helminth nematode schistosoma strongyloides phylogenetic genome expressed
Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

Has reproduction · 87

Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

leaf trimmed species concatenated genome novo reference-assisted
Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

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

Full-text index only

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
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

Full-text index only

RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

Full-text index only

Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

angiosperms animal oryza proteobacteria gene site-heterogeneous codon
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

Full-text index only

Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr
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
Genome-wide survey for biologically functional pseudogenes.

PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

Full-text index only

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
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

Full-text index only

A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

Full-text index only

Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

Has reproduction

SDSD is a distinct taxonomic entity, supported by a mean pairwise average nucleotide identity (ANI) of 99% among isolates

sdsd sdse isolates genomes genome core-genome multilocus
auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups

Has reproduction · 50

auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)

fish genomic auts2 tissues comparative tblastn phylogenetic
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

Full-text index only

3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

Full-text index only

Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation

Experiments

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

The EH1 motif in metazoan transcription factors.

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

Protein co-evolution, co-adaptation and interactions.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

Helminth genomics: The implications for human health.

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

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

Phylogenetic analysis of RhoGAP domain-containing proteins.

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

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

Genome-wide survey for biologically functional pseudogenes.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.