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).

• Targeted capture and massively parallel sequencing of 12 human exomes.

  PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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  Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

  hapmap unrelated na18507 randomly targeted array-based molecular

• Global variation in copy number in the human genome.

  PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

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  A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

  hapmap subset blood snp array karyotyping

• Challenges and standards in integrating surveys of structural variation.

  PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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  There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

  genomic hapmap reference independent comparative snp fosmid

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• 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

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• Sequence polymorphisms cause many false cis eQTLs.

  PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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  Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

  lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl

• 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

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

  PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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  Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

  build chimpanzee unrelated ceph comparative three-color pcr

• 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

• Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

  PMID 16420694 · PMC1382255 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  SNPscan is a web-accessible tool that displays SNP copy number, genotype call, and LOH p-value data together in a single plot per sample

  lymphoblastoid skin ceph genomic snp array pcr

• Variation resources at UC Santa Cruz.

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

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  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 diploid genome sequence of an individual human.

  PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups

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  Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing

  donor huref whole-genome assembly-to-assembly snp

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing