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).

• Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

  PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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  NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

  mandenka worldwide hapmap nat2 full snp analysis

• SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

  PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

  genome predicted target computational snp evolutionary

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding

• High-density SNP genotyping to define beta-globin locus haplotypes.

  PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

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  RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

  genomic rflp subset rflp high-density haploview

• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

  PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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  Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

  lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

  PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

  melanocortin same paired test chromatogram tracediff weak

• Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

  PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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  Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

  autosomal intronic chimpanzee genes comparative human-chimpanzee background

• F-SNP: computationally predicted functional SNPs for disease association studies.

  PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

  genome protein-coding genomic genome-wide non-synonymous exonic nonsense

• The molecular landscape of ASPM mutations in primary microcephaly.

  PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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  ASPM mutations are the most common cause of MCPH

  consanguineous genomic parents one polymorphic sanger family

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

  PMID 19727905 · PMC2946578 · Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2010 · 7 claims · 6 setups

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  Multiple SNPs and haplotypes in FLNB are significantly associated with BMD at lumbar spine, femoral neck, and total hip

  southern same subjects genotype tag taqman dual-energy

• Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

  PMID 16102740 · PMC7124242 · Clinica chimica acta; international journal of clinical chemistry · 2006 · 6 claims · 7 setups

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  The Luminex xMAP system uses spectrally distinct dyed microspheres (up to 100 sets) read by dual lasers to enable simultaneous multiplexed analysis of up to 100 reactions in one vessel.

  genomic apoe hla whole-genome direct oligonucleotide single

• Free energy of DNA duplex formation on short oligonucleotide microarrays.

  PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

  mapping50k_xba240 dgcr hg-u133a pdnn free correlation

• 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

• Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

  PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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  MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

  genomic domestic pooled colorectal snp pooling microsatellite

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• 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