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: hapmap ✕ Assay: candidate ✕ Clear

Designing candidate gene and genome-wide case-control association studies.

PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

Full-text index only

Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

population monozygotic international genome-wide candidate twin
Detecting natural selection by empirical comparison to random regions of the genome.

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

Full-text index only

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
Imputation-based analysis of association studies: candidate regions and quantitative traits.

PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

Full-text index only

Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

study phenotyped genotype bayesian
Targeted capture and massively parallel sequencing of 12 human exomes.

PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

Full-text index only

Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

hapmap unrelated na18507 randomly targeted array-based molecular
Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

PMID 19661472 · PMC2753702 · Stroke · 2009 · 8 claims · 6 setups

Full-text index only

EDN SNP rs1800542 is associated with increased ischemic stroke risk in Caucasian women

international spyw candidate haplotype population
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

Full-text index only

Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

Full-text index only

Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

randomly heirs seattlesnps african resequencing genome-wide tag
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

Full-text index only

Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Software for tag single nucleotide polymorphism selection.

PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

Full-text index only

Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

tgfbr1 encode candidate tag haplotype
Exome sequencing identifies the cause of a mendelian disorder.

PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

Full-text index only

Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

patients chromosomes dhodh utero exome directed sanger
SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

Full-text index only

SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative
Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

Full-text index only

CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

genome-wide genome cohorts array-based snp bac
Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

Full-text index only

Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

build chimpanzee unrelated ceph comparative three-color pcr
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

Full-text index only

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
Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

Full-text index only

Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

pedigrees pedigree genomic ubiad1 microsatellite fine direct
Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

PMID 18212765 · PMC7116808 · Nature clinical practice. Endocrinology & metabolism · 2008 · 8 claims · 8 setups

Full-text index only

Six high-density genome-wide association studies in over 19,000 individuals identified approximately ten T2D-susceptibility loci, including HHEX, IDE, SLC30A8, FTO, CDKAL1, CDKN2A/CDKN2B, and IGF2BP2.

t2d icelandic population tcf7l2 genome-wide linkage candidate-gene
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

Full-text index only

SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission

Experiments

Designing candidate gene and genome-wide case-control association studies.

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

Imputation-based analysis of association studies: candidate regions and quantitative traits.

Targeted capture and massively parallel sequencing of 12 human exomes.

Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

Population genomics of human gene expression.

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

Identification of common genetic variation that modulates alternative splicing.

Software for tag single nucleotide polymorphism selection.

Exome sequencing identifies the cause of a mendelian disorder.

SNPdetector: a software tool for sensitive and accurate SNP detection.

Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

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

Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.