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 15

System / cell line: japanese ✕ Assay: population ✕ Clear

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
Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

estonian hapmap ceu snp tagsnp marker
Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

european-american yoruban japanese case sanger snp linkage
Genotype-phenotype associations: modulation by diet and obesity.

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

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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
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

genomic rmrp family non-finnish sequencing comparative microsatellite
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Designing candidate gene and genome-wide case-control association studies.

PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

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Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

population monozygotic international genome-wide candidate twin
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
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
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
Analysis of sequence conservation at nucleotide resolution.

PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

encode population comparative snp functional
Gene-environment interaction and obesity.

PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

framingham european individuals healthy genome-wide candidate gene-diet
Genomic medicine and developing countries: creating a room of their own.

PMID 18487990 · PMC7096950 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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Developing countries can harness human genetic variation to benefit their populations and economies rather than only importing technology from developed nations.

key polio asthma patients in-depth viral genetic
Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

ulcerans collection snp whole-genome comparative read
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

Has reproduction · 66

Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

blood transcriptomic postmortem saliva gsea machine differential

Experiments

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

Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

Genotype-phenotype associations: modulation by diet and obesity.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Designing candidate gene and genome-wide case-control association studies.

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

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

Analysis of sequence conservation at nucleotide resolution.

Gene-environment interaction and obesity.

Genomic medicine and developing countries: creating a room of their own.

Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.