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).

• V-MitoSNP: visualization of human mitochondrial SNPs.

  PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

  blood blood-derived mtdna standard agarose rflp

• A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

  PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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  Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

  falciparum cloned pyrosequencing pcr

• Improved weight management using genetic information to personalize a calorie controlled diet.

  PMID 17945020 · PMC2151062 · Nutrition journal · 2007 · 7 claims · 4 setups

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  Personalizing a weight-management diet using nutrigenetic test results improves long-term BMI reduction and weight loss maintenance compared to a standard diet.

  buccal patients serum genotyping case-control fasting

• Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

  PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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  A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

  asian random subjects unrelated arms-pcr msei sanger

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

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  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• A modified T-test feature selection method and its application on the HapMap genotype data.

  PMID 18267305 · PMC5054219 · Genomics, proteomics & bioinformatics · 2007 · 7 claims · 4 setups

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  A modified t-test ranking measure, extended to handle nominal SNP genotype data via vector transformation, can effectively rank SNPs by their discriminative capability for population classification.

  hapmap modified f-statistics informativeness

• Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

  PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups

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  A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.

  urothelial hapmap snp plot baf

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• 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

• Visualization of shared genomic regions and meiotic recombination in high-density SNP data.

  PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups

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  SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.

  trio family siblings synthetic snp synthetic mitochondrial