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 116

System / cell line: chimpanzee ✕ Clear

Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
The detection of regions of our genome under selection has increasingly relied on the use of genome scans.

PMID 16197732 · PMC3525123 · Human genomics · 2005 · 8 claims · 3 setups

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Markers linked to a locus under local adaptation show larger variance in allele frequencies across populations (higher FST) than neutral markers

populations common genome snp comparative
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence
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
DNA sequence and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
Adapting to a changing world: RAG genomics and evolution.

PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

rag-1 patients zebrafish vertebrate comparative site-directed clinical
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

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GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

ac133+ excised e14 tissues 2-de lc-ms rt-pcr
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
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
Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

cerevisiae genome chimpanzee hot computational microarray comparative
Genome-wide survey for biologically functional pseudogenes.

PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

human-mouse chimpanzee cross-species maximum-likelihood synteny
Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations in the OAZ3 gene are not a common cause of male infertility

genomic coding inferred oaz3 direct sscp haplotype
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
Automated recognition of retroviral sequences in genomic data--RetroTector.

PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

reference genome chimpanzee red motif whole-genome simulated
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

sequences poly cdna trace pssm-based
Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

european-american yoruban japanese case sanger snp linkage
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

Ensembl 2013.

The detection of regions of our genome under selection has increasingly relied on the use of genome scans.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

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

DNA sequence and analysis of human chromosome 9.

Adapting to a changing world: RAG genomics and evolution.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

Genome assembly comparison identifies structural variants in the human genome.

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

Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

Genome-wide survey for biologically functional pseudogenes.

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

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

Automated recognition of retroviral sequences in genomic data--RetroTector.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

Comparative genomic analysis of prion genes.

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

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.