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).

• 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

• SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

  PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

  melanocortin same paired test chromatogram tracediff weak

• 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

• 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

• SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

  PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools

  genome reference genomic runtime sequence comparative

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

  PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

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  The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

  populations genome genome-wide genome

• Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

  PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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  Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

  genomic commercial plco unrelated targeted long-range genotyping

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study.

  PMID 19963597 · PMC2928997 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 6 claims · 4 setups

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  Developed an imaging genomic browsing system allowing whole genome and entire brain analyses via visual exploration

  mci same voxel-based snp genotype

• Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

  PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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  IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

  population blood genomic hapmap snp survival allele

• Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations.

  PMID 19715579 · PMC2741446 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  Three loci (2q24, 11q23.1-25, 13q14.11-21.33) were identified by both the microsatellite and SNP genome-wide scans

  talana volunteers same ogliastra genome-wide clinical genotype

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• 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

• Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

  PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally

  plasmid genomic bacterial real-time methylation-specific