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 25

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

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
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
Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip.

PMID 17894875 · PMC2211321 · BMC genomics · 2007 · 8 claims · 6 setups

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Efficiency of sequence recovery and accuracy of SNP identification on a species-specific resequencing microarray decline as sequence divergence from the reference increases.

mtdna chimpanzee gorilla atlantic resequencing dideoxy phylogenetic
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
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
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

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The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
What makes species unique? The contribution of proteins with obscure features.

PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

eukaryotic animal cerevisiae homo hmmpfam blast tblastn
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
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
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
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
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
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
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
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
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
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
Inconsistencies in Neanderthal genomic DNA sequences.

PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

genome chimpanzee genomic pcr computational triple pcr

Experiments

Fast-evolving noncoding sequences in the human genome.

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

Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip.

Gene losses during human origins.

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

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

What makes species unique? The contribution of proteins with obscure features.

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

Continued colonization of the human genome by mitochondrial DNA.

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

Web-based resources for comparative genomics.

Absence of the TAP2 human recombination hotspot in chimpanzees.

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

Analysis of the human Alu Ye lineage.

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

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

Heterogeneous genomic molecular clocks in primates.

Inconsistencies in Neanderthal genomic DNA sequences.

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.