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 83

System / cell line: snps ✕ Assay: identification ✕ Clear

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

PMID 17672919 · PMC1973086 · BMC bioinformatics · 2007 · 6 claims · 8 setups

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The Not-N algorithm, incorporated into the Minimum SNPs program, identifies small marker sets diagnostic for user-defined subgroups of genetic variants with 0% false negatives

hcv campylobacter yersinia clostridium snp comparative cgh
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Environmental genome project: focusing on differences to understand the whole.

PMID 12460813 · PMC1241127 · Environmental health perspectives · 2002 · 8 claims · 4 setups

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The EGP has generated a working list of more than 550 environmentally responsive genes involved in pathways such as metabolism, DNA repair, and cell cycle control as candidates for SNP resequencing.

environmentally comparative asthma specified resequencing transgenic genetic
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

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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
Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip.

PMID 17894875 · PMC2211321 · BMC genomics · 2007 · 8 claims · 6 setups

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Efficiency of sequence recovery and accuracy of SNP identification on a species-specific resequencing microarray decline as sequence divergence from the reference increases.

mtdna chimpanzee gorilla atlantic resequencing dideoxy phylogenetic
Olden times: looking back on a career at the NIEHS.

PMID 15289171 · PMC1247486 · Environmental health perspectives · 2004 · 8 claims · 3 setups

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Kenneth Olden served 13 years as director of NIEHS and the National Toxicology Program, the first African American to head an NIH institute

environmentally genome gene microarray transgenic
Use of genomic data in risk assessment.

PMID 11983054 · PMC139345 · Genome biology · 2002 · 8 claims · 4 setups

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New genomic technologies (CGH, SNP analysis, restriction landmark genome scanning, spectral karyotyping, transcript profiling) can be applied to improve risk assessment accuracy

glioma lung animal genome sensitivity expression snp
Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

unrelated same snps haplotype snp haplotype pairwise
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

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NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

tanzanian a549 muheza-tanga sscp pcr restriction
Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

PMID 15234325 · PMC7129141 · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2004 · 7 claims · 3 setups

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Human aminopeptidase N (APN/CD13/ANPEP) is the receptor for human coronavirus 229E (HCoV-229E)

genomic cloned consensus pcr molecular sequence
Emerging strategies and applications of pharmacogenomics.

PMID 15606999 · PMC3500198 · Human genomics · 2004 · 7 claims · 7 setups

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Effective pharmacogenomics requires infrastructure including informed consent processes, accurate phenotypic data collection, high-throughput genotyping technology, and integrated information technology systems.

subjects ethnically patients genome-wide gene case-control
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

PMID 16569251 · PMC1488868 · BMC cancer · 2006 · 7 claims · 4 setups

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Three novel APC germline mutations were identified in Taiwanese subjects: a frameshift deletion at codon 460 (g.1378delG), and two missense substitutions p.V1125A and p.S1126R

genomic taiwanese dhplc pcr sanger
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
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
Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

PMID 19644707 · PMC2778717 · Human genetics · 2009 · 7 claims · 5 setups

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Resequencing of the 97-kb 10q11.2 region identified 241 novel polymorphisms not previously reported in dbSNP

genomic plco hapmap computational targeted long-range genotype
Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

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The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

populations genome genome-wide genome
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

Identification of common genetic variation that modulates alternative splicing.

Environmental genome project: focusing on differences to understand the whole.

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

Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip.

Olden times: looking back on a career at the NIEHS.

Use of genomic data in risk assessment.

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

Human SNPs resulting in premature stop codons and protein truncation.

Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

Emerging strategies and applications of pharmacogenomics.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

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

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

Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.