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 586

System / cell line: allele ✕ Clear

A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

PMID 19956411 · PMC2786888 · Molecular vision · 2009 · 6 claims · 7 setups

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A novel de novo heterozygous nonsense mutation (c.413C>G, p.S138X) in OTX2 causes an early onset retinal dystrophy accompanied by pituitary dysfunction (growth hormone deficiency)

genomic anonymous single direct lca mismatch
Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

unrelated genomic mtmr2 array quantitative sanger
Genetics of autistic disorders: review and clinical implications.

PMID 19941018 · PMC2839494 · European child & adolescent psychiatry · 2010 · 8 claims · 8 setups

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AD are predominantly genetically determined disorders with heritability of around 90%.

families individuals parietal post-mortem genome-wide candidate standard
Searching for SNPs with cloud computing.

PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

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Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

han local short simulated whole-genome cloud
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

isolates genome snp snps multilocus genome bayesian
Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag
Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

PMID 19903357 · PMC3087512 · BMC genetics · 2009 · 7 claims · 6 setups

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LALES Latinos show strong evidence of recent population admixture, primarily from Native American and European ancestries with smaller Asian and African contributions.

lales native genotyping structure hardy-weinberg
Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

PMID 19888477 · PMC2768905 · PloS one · 2009 · 8 claims · 5 setups

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Q-PCR methods yield informative KRAS mutation results even on very fragmented FFPE-DNA where dideoxy-sequencing fails (p<0.0001)

ffpe dideoxy-sequencing taqman-mgb dxs-kras
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic
Analysis of genetic variability and whole genome linkage of whole-brain, subcortical, and ependymal hyperintense white matter volume.

PMID 19834011 · PMC2787844 · Stroke · 2009 · 8 claims · 5 setups

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Whole-brain, subcortical, and ependymal HWM volumes are all highly heritable

mexican extracted same structural genotyping heritability
Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

PMID 19832989 · PMC2770483 · BMC microbiology · 2009 · 8 claims · 5 setups

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The relative proportion of the three Pfmsp1 block2 allelic families (K1, Mad20, RO33) in Dielmo showed no significant temporal fluctuation over a 10-year period (1990-99).

plasmodium dielmo semi-nested direct cross-sectional
Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

PMID 19823582 · PMC2756628 · PloS one · 2009 · 8 claims · 8 setups

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M. tuberculosis isolates with identical DNA fingerprints can harbour substantial genomic diversity at the whole-genome level

tuberculosis whole-genome is6110 spoligotyping
Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise
Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

PMID 19788831 · PMC2819849 · Emerging infectious diseases · 2009 · 8 claims · 5 setups

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NA gene sequences of oseltamivir-resistant viruses (ORVs) form a distinct phylogenetic cluster separate from oseltamivir-sensitive viruses (OSVs)

influenza clinical partial sanger pyrosequencing molecular
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
Detecting natural selection by empirical comparison to random regions of the genome.

PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

ceu genomic simulated long-read snp population
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp
Identification of recombinant human papillomavirus type 16 variants.

PMID 19758676 · PMC2769496 · Virology · 2009 · 8 claims · 5 setups

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Concurrent infection with 8 HPV16 variants (1 prototype/European, 6 recombinant clones, plus later African-2) was detected in a single woman via PCR-based cloning and sequencing

cervical pcr-based recombinant-specific direct

Experiments

A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

Genetics of autistic disorders: review and clinical implications.

Searching for SNPs with cloud computing.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

Analysis of genetic variability and whole genome linkage of whole-brain, subcortical, and ependymal hyperintense white matter volume.

Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Detecting natural selection by empirical comparison to random regions of the genome.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

Identification of recombinant human papillomavirus type 16 variants.