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).

• An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

  PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

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  CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

  individuals hapmap egp snp tag median-joining

• Software for tag single nucleotide polymorphism selection.

  PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

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  Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

  tgfbr1 encode candidate tag haplotype

• Selecting additional tag SNPs for tolerating missing data in genotyping.

  PMID 16259642 · PMC1316880 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  There exists a subset of SNPs (robust tag SNPs) that can distinguish all distinct haplotypes even when up to m SNPs are missing

  simulated hudson's chromosome robust

• SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

  PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

  randomly heirs seattlesnps african resequencing genome-wide tag

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

  hapmap encode enr112 tag cross-validated entropy tagged

• Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

  PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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  IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

  population blood genomic hapmap snp survival allele

• Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families.

  PMID 17900373 · PMC2082241 · BMC dermatology · 2007 · 8 claims · 4 setups

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  This is the first SNP-based genome-wide linkage study of atopic dermatitis performed in an Asian population.

  japanese same genome-wide snp-based family-based targeted

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

  PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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  Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

  genomic commercial plco unrelated targeted long-range genotyping

• 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

• Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

  PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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  Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

  genomic sequenced korean common sanger sequence population

• Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

  PMID 19661472 · PMC2753702 · Stroke · 2009 · 8 claims · 6 setups

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  EDN SNP rs1800542 is associated with increased ischemic stroke risk in Caucasian women

  international spyw candidate haplotype population

• Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.

  PMID 15799788 · PMC1079843 · BMC medical genetics · 2005 · 8 claims · 7 setups

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  Systematic screening of TPH1 exons and promoter region in Taiwanese Han identified five sequence variants: A-1067G, G-347T, T3804A, C27224T, A27237G.

  taiwanese bpd bess arms multiplex

• Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

  PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

  genome chimpanzee sult1a3 est blast-like comparative pairwise

• Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

  PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

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  K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

  a549 western proliferation clonogenic

• Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii.

  PMID 18282098 · PMC2242837 · PLoS pathogens · 2008 · 8 claims · 6 setups

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  A high-throughput ENU mutagenesis screen isolated 165 temperature-sensitive (ts) Toxoplasma growth mutants from ~60,000 clones.

  gondii genomic chemical flow immunofluorescence

• A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

  PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups

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  Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines

  falciparum red northern static rt-pcr

• Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

  PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

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  SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

  african-american thai same study sanger snp genotyping

• Tissue compartment analysis for biomarker discovery by gene expression profiling.

  PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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  TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

  kidney pure serial rt-pcr sage histo-morphometry