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 24

System / cell line: orthologous ✕ Assay: substitution ✕ Clear

Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

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CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

randomly real human-chimpanzee simulated simulation comparative
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
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

tuberculosis putative orthologous genomewide blastp clustal nei-gojobori
Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

autosomal intronic chimpanzee genes comparative human-chimpanzee background
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
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
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
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
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

hg18 zebrafish bystander human-mouse comparative synteny orthologous
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
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

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The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

bovine panel agresearch intact random gene northern
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
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
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups

Has reproduction · 84

The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus

mamiellales ostreococcus tauri shared comparative orthology synteny
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

Experiments

Empirical codon substitution matrix.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Heterotachy in mammalian promoter evolution.

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

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

Getting positive about selection.

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

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

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

Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

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