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).

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

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

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  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

• SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

  PMID 15659576 · PMC548375 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  A microarray-based method allows multiplex SNP genotyping in total human genomic DNA without target amplification or complexity reduction

  unamplified genomic fragmented factor multiplex sequencing poly

• Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

  PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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  3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

  same caucasian cau autosomal snp copy population

• Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

  PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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  Homozygous truncating mutations in PCNT cause Seckel syndrome

  consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• Personalized copy number and segmental duplication maps using next-generation sequencing.

  PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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  mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

  genomes genomic interphase na18507 whole-genome array fluorescence