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).

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Efficacy assessment of SNP sets for genome-wide disease association studies.

  PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

  hapmap affymetrix illumina genome-wide swept comparative

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

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

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  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

• Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

  PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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  Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

  estonian hapmap ceu snp tagsnp marker

• SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

  PMID 18847484 · PMC2576268 · BMC bioinformatics · 2008 · 7 claims · 8 setups

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  SPSmart is a novel tool for accessing and combining large-scale SNP genotype databases with population information

  hapmap perlegen stanford michigan snp cross-database chromosome

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• GABRG1 and GABRA2 as independent predictors for alcoholism in two populations.

  PMID 18818659 · PMC2656604 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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  GABRG1 SNPs and haplotypes are significantly associated with alcohol use disorder (AUD) in both Finnish Caucasians and Plains American Indians

  finnish plains population hapmap snp haplotype ancestry

• What can genome-wide association studies tell us about the genetics of common disease?

  PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

  case gwa simulated literature cochran-armitage computer

• 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

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

  international spyw candidate haplotype population

• Calibrating the performance of SNP arrays for whole-genome association studies.

  PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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  Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

  american liver simulated hapmap snp gene simulation-based

• Investigating the genetic association between ERAP1 and ankylosing spondylitis.

  PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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  The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

  patients cases genotype comparison snp meta-analysis resequencing

• MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

  PMID 16834459 · PMC1502153 · PLoS medicine · 2006 · 8 claims · 8 setups

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  A somatic activating mutation in MPL (W515L, transmembrane domain) is present in 9% (4/45) of JAK2V617F-negative myelofibrosis (MF) patients

  granulocyte hapmap 32d balb sequencing genotyping proliferation

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron

• 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