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).

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

  PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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  SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

  sidcon real mixtures snp re-analysis

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

  PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

  peripheral genomic genotype independent linkage targeted genotyping

• Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

  PMID 19096718 · PMC2603445 · Molecular vision · 2008 · 7 claims · 5 setups

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  CYP1B1 mutations are implicated in POAG among Iranians, notably in the juvenile-onset form

  genomic cyp1b1 poag microarray-based dideoxy sanger

• A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

  PMID 15814067 · PMC3525117 · Human genomics · 2005 · 7 claims · 2 setups

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  Forty-six haplotyping programs were identified and reviewed, split into 43 designed for individual genotype data and three designed for pooled DNA samples.

  pubmed identified literature software