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).

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

  hapmap encode enr112 tag cross-validated entropy tagged

• 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

• An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

  PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

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  CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

  individuals hapmap egp snp tag median-joining

• Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

  PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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  The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

  genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage

• Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

  PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

  simulated real apoe igf2 cubic pairwise haplotype

• Power analysis for genome-wide association studies.

  PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

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  Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

  hapmap power pairwise tag

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

  PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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  ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

  hapmap combined coriell ceu allele-specific linear one-sample

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• 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

• MutDB: update on development of tools for the biochemical analysis of genetic variation.

  PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

  proteins mutdb nonsynonymous genes sequence web functional

• An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

  PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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  Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

  unrelated shanghai tsnps snp allele linkage

• Sequence variation in the human transcription factor gene POU5F1.

  PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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  POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

  genomic multi-species inferred international resequencing comparative haplotype

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• Negative emotionality: monoamine oxidase B gene variants modulate personality traits in healthy humans.

  PMID 19657584 · PMC3653168 · Journal of neural transmission (Vienna, Austria : 1996) · 2009 · 7 claims · 7 setups

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  MAOB SNPs rs10521432 and rs6651806 are significantly associated with Negative Emotionality in healthy volunteers

  healthy genotype maoa snp multidimensional profile

• Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

  PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

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  SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

  african-american thai same study sanger snp genotyping