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 34

System / cell line: snp ✕ Assay: real-time ✕ Clear

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
SNP-specific extraction of haplotype-resolved targeted genomic regions.

PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

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SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

genomic diploid quantitative sanger low
The FAS gene, brain volume, and disease progression in Alzheimer's disease.

PMID 19766542 · PMC3100774 · Alzheimer's & dementia : the journal of the Alzheimer's Association · 2010 · 8 claims · 4 setups

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The minor (T) allele of rs1468063 in FAS is significantly associated with faster AD progression after permutation-based multiple-testing correction

peripheral longitudinally same subset snp survival permutation
A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

individuals mother-father-child transcribed snp quantitative multiplex
Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

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DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

nuclear same sh-sy5y snp haplotype-based quantitative
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

representative illumina six snp serial concentration
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

PMID 19864672 · PMC2793117 · The New England journal of medicine · 2009 · 7 claims · 7 setups

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A homozygous CARD9 point mutation (Q295X, premature termination codon) is associated with autosomal recessive susceptibility to chronic mucocutaneous candidiasis.

family patients peripheral-blood peripheral snp microsatellite sanger
Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

irish iccss postmortem genomic snp haplotype logistic
Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

PMID 19681120 · PMC3430375 · Genes, chromosomes & cancer · 2009 · 8 claims · 5 setups

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PCDH10 promoter hypermethylation is a frequent event in invasive cervical cancer

invasive lines normal cervical snp methylation-specific bisulphite
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
Increased levels of human beta-defensins mRNA in sexually HIV-1 exposed but uninfected individuals.

PMID 18991618 · PMC4126611 · Current HIV research · 2008 · 8 claims · 5 setups

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ESN individuals show significantly higher HBD-2 and HBD-3 mRNA copy numbers in oral mucosa than healthy controls (HC)

oral vaginal endocervical peripheral real-time pcr-rflp sequencing
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

genomic huvec microarray solid-phase real-time
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

leukocytes leukocyte-derived archived comparison whole-genome quantitative snp
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
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

Experiments

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

SNP-specific extraction of haplotype-resolved targeted genomic regions.

The FAS gene, brain volume, and disease progression in Alzheimer's disease.

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

A homozygous CARD9 mutation in a family with susceptibility to fungal infections.

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Allele quantification using molecular inversion probes (MIP).

Increased levels of human beta-defensins mRNA in sexually HIV-1 exposed but uninfected individuals.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

Genetic variation in PARL influences mitochondrial content.

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