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 25

System / cell line: genome ✕ Assay: odds ✕ Clear

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

dbsnp best-hit omicia hgmd genome-wide correlation disease
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
Improving the specificity of exon prediction using comparative genomics.

PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

human-mouse human-dog genome simulated comparative single-genome simulated
Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

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CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

genome-wide genome cohorts array-based snp bac
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
Prostate cancer genomics: towards a new understanding.

PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

germline families african-american combined genome-wide linkage admixture
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

cases patients postmortem whole-genome cox linear
Current and future directions in genomics of amyotrophic lateral sclerosis.

PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

american sals dutch irish genome laser expression
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
Genetics of autistic disorders: review and clinical implications.

PMID 19941018 · PMC2839494 · European child & adolescent psychiatry · 2010 · 8 claims · 8 setups

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AD are predominantly genetically determined disorders with heritability of around 90%.

families individuals parietal post-mortem genome-wide candidate standard
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

genome vertebrate multi-species whole-genome conservation non-synonymous
What can genome-wide association studies tell us about the genetics of common disease?

PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

case gwa simulated literature cochran-armitage computer
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

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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
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.

PMID 15743496 · PMC1064127 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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A common BRCA1 haplotype (haplotype 2, C A G G) is associated with a modest increase in sporadic breast cancer risk

individuals nested same nurses whole-gene snp statistical
Analytical code sharing practices in biomedical research.

PMID 38983240 · PMC11232620 · PeerJ. Computer science · 2024 · 8 claims · 4 setups

Has reproduction · 92

Nearly half (49.9%) of 453 examined biomedical manuscripts failed to share the analytical code used to generate their results

biomedical manuscripts journals subset bibliometric chi-square odds
An efficient method for multi-locus molecular haplotyping.

PMID 17158153 · PMC1802573 · Nucleic acids research · 2007 · 7 claims · 6 setups

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A novel molecular haplotyping method using limiting dilution, aliquot pre-screening, and tiling reconstruction can resolve haplotypes spanning many loci over long distances from a single individual's DNA.

single agarose-embedded genotyping multiplexed monoplex primer-extension
Replication by the Epistasis Project of the interaction between the genes for IL-6 and IL-10 in the risk of Alzheimer's disease.

PMID 19698145 · PMC2744667 · Journal of neuroinflammation · 2009 · 8 claims · 4 setups

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IL6 rs2069837 AA x IL10 rs1800871 CC interaction is associated with increased AD risk (synergy factor 1.63)

blood-derived pooled snp genome-wide logistic
Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

Has reproduction · 79

Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

studies taiwan twb ded meta-analysis genome-wide conditional

Experiments

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

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

Improving the specificity of exon prediction using comparative genomics.

Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

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

Prostate cancer genomics: towards a new understanding.

Sequence context affects the rate of short insertions and deletions in flies and primates.

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

Current and future directions in genomics of amyotrophic lateral sclerosis.

Genetic and functional association of FAM5C with myocardial infarction.

Genetics of autistic disorders: review and clinical implications.

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

What can genome-wide association studies tell us about the genetics of common disease?

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

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.

Analytical code sharing practices in biomedical research.

An efficient method for multi-locus molecular haplotyping.

Replication by the Epistasis Project of the interaction between the genes for IL-6 and IL-10 in the risk of Alzheimer's disease.

Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.