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).

• Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

  PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

  representative illumina six snp serial concentration

• Modeling genetic inheritance of copy number variations.

  PMID 18832372 · PMC2588508 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  A joint HMM framework for parents-offspring trios significantly improves CNV call rates and boundary inference accuracy compared to existing methods.

  simulated parent-offspring hapmap hmm-based snp genotype

• Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

  PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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  ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

  hapmap combined coriell ceu allele-specific linear one-sample

• Allele quantification using molecular inversion probes (MIP).

  PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

  reference ffpe lines na18573 mip restriction quantitative

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• 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

• Functional copy-number alterations in cancer.

  PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups

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  RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.

  pleomorphic hapmap large snp computational

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species

• Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

  PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

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  Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

  pedigrees pedigree genomic ubiad1 microsatellite fine direct

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

  PMID 18212765 · PMC7116808 · Nature clinical practice. Endocrinology & metabolism · 2008 · 8 claims · 8 setups

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  Six high-density genome-wide association studies in over 19,000 individuals identified approximately ten T2D-susceptibility loci, including HHEX, IDE, SLC30A8, FTO, CDKAL1, CDKN2A/CDKN2B, and IGF2BP2.

  t2d icelandic population tcf7l2 genome-wide linkage candidate-gene

• A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

  PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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  SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

  teds diagnosed ceph snp individual transmission

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence