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).

• PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

  PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

  Full-text index only

  The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

  individually reference equimolar independently snp reference pooled

• Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

  PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

  genomic pools training siddt individual pooled k-correction

• 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

  Full-text index only

  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

• SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

  PMID 16262895 · PMC1280925 · BMC genomics · 2005 · 8 claims · 5 setups

  Full-text index only

  Poorly performing SNPs (NoCall rate ≥25%) fail primarily due to inadequate training/localization of the MPAM statistical model call zone, not detection filter failure

  genomic genotype genotyped chromosomal snp clustering mendelian

• Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

  PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups

  Full-text index only

  Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA

  pooled pool snps snp snapshot individual

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• The UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• Chips to hits.

  PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

  individual yeast pools lncap cell-based affymetrix automated