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

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
FeatureScan: revealing property-dependent similarity of nucleotide sequences.

PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

randomly fully same chimpanzee signal-theoretic featurescan blast
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
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
Reference based annotation with GeneMapper.

PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

orthologous human-mouse chicken encode reference-based multi-species reciprocal
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
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
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

liver chimpanzee h-invitational tar genome blastn secondary
Assessing the gene space in draft genomes.

PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

caenorhabditis toxoplasma homo briggsae cegma blast tblastn
Better smelling through genetics: mammalian odor perception.

PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

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Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

mammals subjects v1r trpc2 comparative genetic targeted
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
Sex-biased evolutionary forces shape genomic patterns of human diversity.

PMID 18818765 · PMC2538571 · PLoS genetics · 2008 · 7 claims · 5 setups

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X-linked diversity is higher than the neutral expectation (0.75) relative to autosomal diversity in all six sampled human populations

humans population simulated computational resequencing coalescent-based coalescent
Genetic variation in an individual human exome.

PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

huref genes subset whole-genome allele functional
Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups

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Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.

genomic myoc poag pcr amino clinical
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
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence
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
Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

PMID 19682372 · PMC2735741 · BMC evolutionary biology · 2009 · 7 claims · 7 setups

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Major NLRP genes duplicated before the divergence of mammals, with lineage-specific duplications in primates (NLRP7, NLRP11) and rodents (Nlrp1, Nlrp4, Nlrp9)

mammalian cattle oocyte-expressed genome phylogenetic syntenic functional

Experiments

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

FeatureScan: revealing property-dependent similarity of nucleotide sequences.

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

Heterotachy in mammalian promoter evolution.

Reference based annotation with GeneMapper.

Personalized genomic medicine with a patchwork, partially owned genome.

Inconsistencies in Neanderthal genomic DNA sequences.

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

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

Assessing the gene space in draft genomes.

Better smelling through genetics: mammalian odor perception.

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

Sex-biased evolutionary forces shape genomic patterns of human diversity.

Genetic variation in an individual human exome.

Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

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

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

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

Evolution and functional divergence of NLRP genes in mammalian reproductive systems.