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).

• Genomic mutation rates: what high-throughput methods can tell us.

  PMID 19644920 · PMC2952423 · BioEssays : news and reviews in molecular, cellular and developmental biology · 2009 · 8 claims · 8 setups

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  High-throughput DNA analyses yield genome mutation rate estimates markedly higher than those obtained with pre-genomic strategies

  cerevisiae elegans melanogaster mammals fluctuation mutation indirect

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide

• An enhanced single base extension technique for the analysis of complex viral populations.

  PMID 19834618 · PMC2759544 · PloS one · 2009 · 8 claims · 7 setups

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  The MDAP single base extension microarray platform measures nucleotide frequency at each genomic position in a complex population without requiring prior knowledge of candidate SNPs

  transcribed poliovirus array-bound array single oligonucleotide sbe

• Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

  PMID 18752264 · PMC2577713 · Human mutation · 2008 · 8 claims · 4 setups

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  40% (16/40) of WWS families in this diverse cohort received a molecular diagnosis with mutations in POMT1, POMT2, FKRP or FCMD

  genomic pomt2 population genome-wide pcr multiplex

• Molecular characterization of retinitis pigmentosa in Saudi Arabia.

  PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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  The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

  blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional

• Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

  PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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  C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

  chimpanzee intergenic genome-wide chi-square nucleotide-content

• Atrial natriuretic peptide frameshift mutation in familial atrial fibrillation.

  PMID 18614783 · PMC2518320 · The New England journal of medicine · 2008 · 7 claims · 5 setups

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  A heterozygous frameshift mutation in NPPA (encoding atrial natriuretic peptide, ANP) causes familial atrial fibrillation

  family plasma atria genome-wide fine exon

• The EPHA2 gene is associated with cataracts linked to chromosome 1p.

  PMID 19005574 · PMC2582197 · Molecular vision · 2008 · 5 claims · 5 setups

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  A heterozygous c.2842G>T (p.G948W) mutation in EPHA2 exon 17 causes autosomal dominant posterior polar cataracts in family Mu

  family case-control genome-wide str pcr

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

  PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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  Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

  family p2ry5 affected snp microsatellite sanger

• Human genome research in China.

  PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

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  China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

  genome chinese high-risk nb4 large-scale mutation positional

• Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

  PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.

  blood v34a cos1 cv1 small genome-wide strip

• Emerging strategies and applications of pharmacogenomics.

  PMID 15606999 · PMC3500198 · Human genomics · 2004 · 7 claims · 7 setups

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  Effective pharmacogenomics requires infrastructure including informed consent processes, accurate phenotypic data collection, high-throughput genotyping technology, and integrated information technology systems.

  subjects ethnically patients genome-wide gene case-control

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• Analysis of the human Alu Ye lineage.

  PMID 15725352 · PMC554112 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Two new Alu subfamilies, Ye4 and Ye6, were discovered, complementing the previously described Ye5 subfamily.

  draft genomic non-human geographically blast sequence pcr