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 17

System / cell line: clone ✕ Assay: phylogenetic ✕ Clear

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
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
Structure of the intergenic spacers in chicken ribosomal DNA.

PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

Has reproduction · 80

Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

faecal mcra pure pcr rflp 16s
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

pad phylogenetic est est-based
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

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The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
A Deluge of Complex Repeats: The Solanum Genome.

PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

Has reproduction · 94

~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

tuberosum orthologous identified de-novo genome-wide transcriptional
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
Evolutionary toggling of the MAPT 17q21.31 inversion region.

PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

chimpanzee lymphoblastoid donor whole-genome reciprocal bac
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

faecal rsr 16s sargasso shotgun blastn-based 16s
Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

serum hvr1 svr rt-pcr shannon hamming
New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

skin cloned mixed-type gene nested sequencing molecular

Experiments

DNA sequence and analysis of human chromosome 9.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Structure of the intergenic spacers in chicken ribosomal DNA.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

Molecular analysis of Plasmodium ovale variants.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

A Deluge of Complex Repeats: The Solanum Genome.

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

Evolutionary toggling of the MAPT 17q21.31 inversion region.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.