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).

• KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

  PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

  Has reproduction · 42

  KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

  small snps individual hg002 alignment-free kmer-based genotyping

• Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

  PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups

  Full-text index only

  Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm

  unrelated same haplotype caucasian snp haplotype group

• Genotype-phenotype associations: modulation by diet and obesity.

  PMID 19037211 · PMC2771769 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 7 setups

  Full-text index only

  Obesity modulates the association between APOE genotype and fasting insulin/glucose levels in men, with obese APOE4 carriers showing higher insulin and glucose than other obese genotype groups.

  framingham spanish caucasian population apoe edn1 lpl

• A common haplotype within the PON1 promoter region is associated with sporadic ALS.

  PMID 18618303 · PMC2739087 · Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases · 2008 · 7 claims · 6 setups

  Full-text index only

  Two SNPs (rs987539 in PON2 intron 6 and rs2074351 upstream of PON1 exon 2) within the paraoxonase gene cluster are significantly associated with susceptibility to sporadic ALS

  genomic case-control sporadic serum snp allelic sliding-window

• CCL genes in multiple sclerosis and systemic lupus erythematosus.

  PMID 18602166 · PMC5301077 · Journal of neuroimmunology · 2008 · 7 claims · 5 setups

  Full-text index only

  Previously suggested borderline CCL marker/haplotype associations with MS are rejected after Bonferroni correction for multiple testing

  genomic patients 17q11.2-q12 buccal snp linkage hardy-weinberg

• Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

  PMID 18544707 · PMC2518503 · Diabetes · 2008 · 8 claims · 4 setups

  Full-text index only

  None of the selected GWAS-identified SNPs individually were associated with increased diabetes incidence in the DPP cohort

  dpp snp cox oral

• mtDNA nt13708A variant increases the risk of multiple sclerosis.

  PMID 18270557 · PMC2217590 · PloS one · 2008 · 8 claims · 5 setups

  Full-text index only

  The mtDNA nt13708 G/A polymorphism (nt13708A allele) is significantly associated with increased risk of MS (OR=1.71, P=0.0002) across three well-matched European cohorts.

  peripheral pooled mtdna snp meta-analysis complete

• Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

  PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

  Full-text index only

  rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

  irish iccss postmortem genomic snp haplotype logistic

• Apolipoprotein e, alcohol consumption, and risk of ischemic stroke: the Framingham Heart Study revisited.

  PMID 19717024 · PMC2743951 · Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association · 2009 · 8 claims · 6 setups

  Full-text index only

  ApoE E4 allele does not significantly modify the association between alcohol consumption and risk of ischemic stroke in subjects <65 years

  framingham plasma genotyping structured clinical

• Nicotinamide N-methyl transferase (NNMT) gene polymorphisms and risk for spina bifida.

  PMID 18553462 · PMC2630518 · Birth defects research. Part A, Clinical and molecular teratology · 2008 · 7 claims · 3 setups

  Full-text index only

  NNMT was identified in a genome-wide linkage scan (Souto et al., 2005) as an important regulator of plasma homocysteine concentration in a Spanish population.

  infants infant same snp case-control haplotype

• Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

  PMID 16848906 · PMC1543620 · Molecular pain · 2006 · 8 claims · 5 setups

  Full-text index only

  COMT SNP5 (rs740603, intron 1) shows significant association with maximum post-operative pain rating

  surgical candidate haplotype allele

• Weak or no association of TCF7L2 variants with Type 2 diabetes risk in an Arab population.

  PMID 18655717 · PMC2515290 · BMC medical genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  rs7903146 T allele frequency does not differ significantly between Saudi T2D cases and controls (OR 1.04, 95% CI 0.86-1.27, P=0.675)

  peripheral saudi genotype subset snp case-control haplotype

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians.

  PMID 18433491 · PMC2375899 · BMC cancer · 2008 · 6 claims · 4 setups

  Full-text index only

  MDM2 SNP309 T/G genotype is not associated with DLBCL or NHL onset, diagnosis, or age of onset in central European Caucasians, including in pre-menopausal women

  genomic nhl pcr case-control survival

• The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample.

  PMID 19800201 · PMC2783814 · Schizophrenia research · 2009 · 8 claims · 7 setups

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  Common alleles at DTNBP1 SNPs, particularly rs760761, are associated with schizophrenia in the ICCSS sample

  irish chimpanzee dtnbp1 snp haplotype case

• 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

• 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

• Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

  PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

  Full-text index only

  The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

  genomic same pooled pcr-rflp pcr-based cross-tabulation

• Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

  PMID 18567820 · PMC2518507 · Diabetes · 2008 · 8 claims · 5 setups

  Full-text index only

  CDC123/CAMK1D rs12779790 risk allele (homozygous) is associated with decreased insulinogenic index, corrected insulin response (CIR), and AUC-insulin/AUC-glucose ratio, indicating impaired insulin release

  inter99 same taqman oral general

• Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

  PMID 19750224 · PMC2735778 · PLoS pathogens · 2009 · 7 claims · 5 setups

  Full-text index only

  The IRGM −261TT genotype is negatively associated with (protective against) pulmonary TB caused by M. tuberculosis

  pulmonary tuberculosis reporter genotyped case-control gene spoligotyping