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 9

System / cell line: orthologs ✕ Assay: nonsynonymous ✕ Clear

Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

sequence genes proteins sequences snp interspecies sequence
Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

orthologous hox concatenated intronic sliding comparative molecular
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
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

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

yeast familial human-mouse comparative gene mutation
Evolutionary history of the UCP gene family: gene duplication and selection.

PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

vertebrate ucp human-mouse ucp1 sequence phylogenetic gene
Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

brasiliensis gp43 ratio codon-based mutational
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional

Experiments

Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

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

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.

Evolutionary history of the UCP gene family: gene duplication and selection.

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Identification and characterization of insect-specific proteins by genome data analysis.