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 115

System / cell line: chimpanzee ✕ Clear

Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled
Continued colonization of the human genome by mitochondrial DNA.

PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

homo genomic chimpanzee genome genome-wide pcr sanger
Absence of the TAP2 human recombination hotspot in chimpanzees.

PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

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The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

western haplotype males simulated resequencing ld-based sperm
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
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
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
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic
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
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
A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.

PMID 19942684 · PMC2817474 · Nucleic acids research · 2010 · 8 claims · 7 setups

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Exogenous RPA4 expression does not support chromosomal DNA replication and causes cell-cycle arrest in G2/M

hela mammalian rpa4 western flow immunofluorescence
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

3'-utr mirbase hapmap comparative snp mirna
Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

PMID 41882679 · PMC13019944 · Genome biology · 2026 · 8 claims · 7 setups

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The majority of long-range intronic RNA duplexes detected genome-wide are mediated by inverted Alu-repeat elements.

k562 hek293t chimpanzee computational splash eclip-seq
Ensembl 2005.

PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.

chicken genomes vertebrate annotated experimental gene pairwise
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
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
Lineage-specific gene duplication and loss in human and great ape evolution.

PMID 15252450 · PMC449870 · PLoS biology · 2004 · 8 claims · 7 setups

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Genome-wide interspecies cDNA aCGH can identify lineage-specific gene copy number changes across five hominoid species

bonobo chimpanzee gorilla orangutan cdna fluorescence literature-based
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
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
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

Web-based resources for comparative genomics.

Comparative genomics comes of age.

Continued colonization of the human genome by mitochondrial DNA.

Absence of the TAP2 human recombination hotspot in chimpanzees.

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

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

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

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

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

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

A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

Ensembl 2005.

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

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

Lineage-specific gene duplication and loss in human and great ape evolution.

Analysis of the human Alu Ye lineage.

Heterogeneous genomic molecular clocks in primates.

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