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).

• Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

  PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

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  CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

  genome-wide genome cohorts array-based snp bac

• Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

  PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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  Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

  peripheral array custom snp

• Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

  PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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  Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

  fresh-frozen same banked resected array mutational pcr

• Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

  PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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  graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

  neuroblastoma same normal megabladder acgh bac principal

• Relative impact of nucleotide and copy number variation on gene expression phenotypes.

  PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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  SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

  lymphoblastoid same computational subset gene snp array

• 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

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density