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).

Publications 1.3k Datasets 392.5k Experiments 73

System / cell line: snp ✕ Assay: selection ✕ Clear

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

randomly heirs seattlesnps african resequencing genome-wide tag
Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

population blood genomic hapmap snp survival allele
Software for tag single nucleotide polymorphism selection.

PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

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Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

tgfbr1 encode candidate tag haplotype
Supervised learning-based tagSNP selection for genome-wide disease classifications.

PMID 18366619 · PMC2386071 · BMC genomics · 2008 · 7 claims · 2 setups

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SRFA (Supervised Recursive Feature Addition) is a novel feature selection method combining supervised learning and statistical redundancy measures for SNP selection

micc narac snp
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

PMID 15774022 · PMC1274256 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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SNPHunter allows ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (physical position, function class, flanking sequences at user-defined lengths, heterozygosity) from NCBI dbSNP

ncbi candidate tnf batch-mode snp gene
Evolutionary algorithms for the selection of single nucleotide polymorphisms.

PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).

simulated mhc evolutionary multiobjective
Selecting additional tag SNPs for tolerating missing data in genotyping.

PMID 16259642 · PMC1316880 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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There exists a subset of SNPs (robust tag SNPs) that can distinguish all distinct haplotypes even when up to m SNPs are missing

simulated hudson's chromosome robust
An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

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CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

individuals hapmap egp snp tag median-joining
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
A model-based approach to selection of tag SNPs.

PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

hapmap encode enr112 tag cross-validated entropy tagged
Sequence variation in the human transcription factor gene POU5F1.

PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

genomic multi-species inferred international resequencing comparative haplotype
QuickSNP: an automated web server for selection of tagSNPs.

PMID 17517769 · PMC1933212 · Nucleic acids research · 2007 · 7 claims · 3 setups

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QuickSNP is a freely available automated web server for selecting tagSNPs from a chromosomal region, genes within a region, or a specified gene list, with a gene-centric selection option

genes selected chromosome automated gene-centric tagsnp
Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

PMID 18212765 · PMC7116808 · Nature clinical practice. Endocrinology & metabolism · 2008 · 8 claims · 8 setups

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Six high-density genome-wide association studies in over 19,000 individuals identified approximately ten T2D-susceptibility loci, including HHEX, IDE, SLC30A8, FTO, CDKAL1, CDKN2A/CDKN2B, and IGF2BP2.

t2d icelandic population tcf7l2 genome-wide linkage candidate-gene
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
A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

individuals sequence resequencing snps targeted sequence genotype
Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

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SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

african-american thai same study sanger snp genotyping
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

genomic dbsnp tnt duplex bioinformatic
HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

white same hapmap snp haplotype tagging
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

unrelated shanghai tsnps snp allele linkage

Experiments

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

Software for tag single nucleotide polymorphism selection.

Supervised learning-based tagSNP selection for genome-wide disease classifications.

SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

Evolutionary algorithms for the selection of single nucleotide polymorphisms.

Selecting additional tag SNPs for tolerating missing data in genotyping.

An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

Single nucleotide polymorphism-based genome-wide linkage analysis in Japanese atopic dermatitis families.

A model-based approach to selection of tag SNPs.

Sequence variation in the human transcription factor gene POU5F1.

QuickSNP: an automated web server for selection of tagSNPs.

Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.