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 20

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

The Neandertal genome and ancient DNA authenticity.

PMID 19661919 · PMC2725275 · The EMBO journal · 2009 · 8 claims · 6 setups

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Only direct assays of DNA sequence positions where Neandertals differ from all contemporary humans can reliably estimate human contamination.

neandertal pcr high-throughput genome
Fast-evolving noncoding sequences in the human genome.

PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

chimpanzee genome hapmap comparative genomic segmental
Evolution of genomic sequence inhomogeneity at mid-range scales.

PMID 19891785 · PMC2779198 · BMC genomics · 2009 · 7 claims · 3 setups

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MRI regions have comparable levels of de novo mutations to control genomic sequences with average base composition.

chimpanzee population genome whole-genome snp indel
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
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
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
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
Bushes in the tree of life.

PMID 17105342 · PMC1637082 · PLoS biology · 2006 · 8 claims · 8 setups

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Bush-shaped clades, produced by short internal stems and long external branches, resist phylogenetic resolution regardless of the amount of conventional data collected.

chimpanzee elephant coelacanth metazoan multi-gene rare nuclear
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
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
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
A genome-wide screen for noncoding elements important in primate evolution.

PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.

phastcons global genome accelerated comparative targeted fisher's
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
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
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
RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

palestinian genomic probands lymphoblasts targeted sanger pcr
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

Experiments

The Neandertal genome and ancient DNA authenticity.

Fast-evolving noncoding sequences in the human genome.

Evolution of genomic sequence inhomogeneity at mid-range scales.

Heterogeneous genomic molecular clocks in primates.

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

Heterotachy in mammalian promoter evolution.

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

Bushes in the tree of life.

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

Getting positive about selection.

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

A genome-wide screen for noncoding elements important in primate evolution.

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

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

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

RPS4Y gene family evolution in primates.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

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.