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 12

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

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

chimpanzee intergenic genome-wide chi-square nucleotide-content
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
Patterns and rates of intron divergence between humans and chimpanzees.

PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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Intron divergence (Ki) is strongly positively correlated with intron length

orthologous genome whole-genome cpg recombination
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
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
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

genome random cd4+ six average mutual chip-seq
Periodicity of SNP distribution around transcription start sites.

PMID 16579865 · PMC1448210 · BMC genomics · 2006 · 8 claims · 6 setups

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SNP density around TSS shows a 146-nucleotide periodicity

genome human-chimpanzee tss promoter snp sequence cpg
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
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

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

chromosome genomic pbmc multi-species phylogenetic bisulphite
Genome-wide analysis of the human Alu Yb-lineage.

PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

genome genomic non-human yb7 computational pcr-based pcr
Analysis of the human Alu Ye lineage.

PMID 15725352 · PMC554112 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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Two new Alu subfamilies, Ye4 and Ye6, were discovered, complementing the previously described Ye5 subfamily.

draft genomic non-human geographically blast sequence pcr
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

Experiments

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

Heterogeneous genomic molecular clocks in primates.

Patterns and rates of intron divergence between humans and chimpanzees.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

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

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

Periodicity of SNP distribution around transcription start sites.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

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

Genome-wide analysis of the human Alu Yb-lineage.

Analysis of the human Alu Ye lineage.

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