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).

• Allele quantification using molecular inversion probes (MIP).

  PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

  reference ffpe lines na18573 mip restriction quantitative

• CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

  PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

  Full-text index only

  CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

  normal genomic sk-br-3 cancer snp quantitative allele-specific

• Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

  PMID 19043545 · PMC2581785 · PLoS genetics · 2008 · 7 claims · 4 setups

  Full-text index only

  A GWA study using serum metabolomics identifies SNPs associated with metabolite concentrations, explaining up to 12% of variance for single metabolites

  kora fasting genome-wide targeted metabolite

• Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

  PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

  Full-text index only

  Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

  individuals mother-father-child transcribed snp quantitative multiplex

• Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis.

  PMID 15716623 · PMC2808565 · Journal of Korean medical science · 2005 · 8 claims · 8 setups

  Full-text index only

  CF should be suspected in Korean/Asian children with chronic respiratory symptoms despite its rarity in Asian populations

  korean family bronchial quantitative sweat cftr

• Global variation in copy number in the human genome.

  PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

  Full-text index only

  A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

  hapmap subset blood snp array karyotyping

• Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

  PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

  Full-text index only

  DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

  nuclear same sh-sy5y snp haplotype-based quantitative

• Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

  PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

  representative illumina six snp serial concentration

• Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

  PMID 18768181 · PMC2699582 · Atherosclerosis · 2009 · 8 claims · 6 setups

  Full-text index only

  COX-2 promoter SNP rs689466 is associated with lower coronary calcified plaque (CorCP)

  whole-blood-derived subjects dhs unrelated snp coronary carotid

• SNP-specific extraction of haplotype-resolved targeted genomic regions.

  PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

  Full-text index only

  SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

  genomic diploid quantitative sanger low

• Calibrating the performance of SNP arrays for whole-genome association studies.

  PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

  american liver simulated hapmap snp gene simulation-based

• 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

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter

• 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

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

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

  Full-text index only

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

  genomic domestic pooled colorectal snp pooling microsatellite

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

  Full-text index only

  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• 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

• Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

  PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

  Full-text index only

  SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

  stroke-free elderly african-american cardiovascular genome-wide direct expression

• A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

  PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

  genomic pgp1 skin fibroblasts padlock quantitative gene

• Clinical practice and genetic counseling for cystic fibrosis and CFTR-related disorders.

  PMID 19092437 · PMC2810953 · Genetics in medicine : official journal of the American College of Medical Genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  CFTR-related disorders form a disease spectrum ranging from isolated congenital absence of the vas deferens (CAVD) to multiorgan classic cystic fibrosis (CF).

  patients newborns sweat transepithelial cftr