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).

• Pharmacogenomics of gemcitabine: can genetic studies lead to tailor-made therapy?

  PMID 17595663 · PMC2360307 · British journal of cancer · 2007 · 8 claims · 14 setups

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  A SNP in the cytidine deaminase (CDA) gene (208G>A, haplotype *3) decreases gemcitabine clearance, increases Cmax/AUC, and increases neutropenia risk when gemcitabine is combined with platinum drugs or 5-FU

  japanese paraffin-embedded tumour recombinant prospective immunohistochemistry pcr

• 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

• Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

  PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

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  Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

  healthy genomic genotype trial randomized snp haplotype

• Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

  PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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  About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

  genomic japanese reference snp concentration agarose

• Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

  PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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  Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

  estonian hapmap ceu snp tagsnp marker

• Gene-environment interaction and obesity.

  PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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  Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

  framingham european individuals healthy genome-wide candidate gene-diet

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• 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

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

  PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

  ulcerans collection snp whole-genome comparative read

• Designing candidate gene and genome-wide case-control association studies.

  PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

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  Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

  population monozygotic international genome-wide candidate twin

• Genomic medicine and developing countries: creating a room of their own.

  PMID 18487990 · PMC7096950 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  Developing countries can harness human genetic variation to benefit their populations and economies rather than only importing technology from developed nations.

  key polio asthma patients in-depth viral genetic

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• Outlook on Thailand's genomics and computational biology research and development.

  PMID 18654621 · PMC2446437 · PLoS computational biology · 2008 · 8 claims · 8 setups

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  Thai government policy support, infrastructure investment, education programs, and human resource development have substantially advanced genomics and bioinformatics research capacity in Thailand

  burkholderia rice healthy thai genome snp htsnp

• 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

• Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

  PMID 19903357 · PMC3087512 · BMC genetics · 2009 · 7 claims · 6 setups

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  LALES Latinos show strong evidence of recent population admixture, primarily from Native American and European ancestries with smaller Asian and African contributions.

  lales native genotyping structure hardy-weinberg