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).

• Social and ethical implications of genomics, race, ethnicity, and health inequities.

  PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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  Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

  population prostate non-small-cell breast genome-wide gene somatic

• Association of adiponectin gene polymorphisms with type 2 diabetes in an African American population enriched for nephropathy.

  PMID 19056609 · PMC2628626 · Diabetes · 2009 · 8 claims · 5 setups

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  SNP rs182052 in intron 1 of ADIPOQ is associated with diabetic nephropathy in African Americans

  african snp sequencing admixture

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

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

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  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

• Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II.

  PMID 19881469 · PMC4511341 · Journal of human genetics · 2009 · 8 claims · 6 setups

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  Screening all 72 exons of USH2A (long isoform) identifies significantly more mutations than screening only the short-isoform exons 1-21

  genomic ush2 ush2a sscp audiological ophthalmological

• Genetics and functional genomics of type 2 diabetes mellitus.

  PMID 14659011 · PMC329413 · Genome biology · 2003 · 7 claims · 5 setups

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  Genome-wide transcription profiling of diabetic skeletal muscle reveals coordinated downregulation of oxidative phosphorylation genes, converging on PGC1α as a central regulator.

  skeletal population microarray real-time genetic

• Genome-wide association studies in neurological disorders.

  PMID 18940696 · PMC2824165 · The Lancet. Neurology · 2008 · 8 claims · 6 setups

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  GWAS can identify common genetic variability associated with a trait across the whole genome, avoiding the bias and low throughput of candidate-gene studies

  icelandic german north sclerosis genome-wide multistage

• 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

• 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

• Glucosidase-beta variations and Lewy body disorders.

  PMID 18829375 · PMC2970615 · Parkinsonism & related disorders · 2009 · 8 claims · 1 setups

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  GBA pathogenic mutations were found in 3% of LBD cases versus 1% of controls, a non-significant difference (OR 3.0, 95% CI 0.3–29, p=0.3)

  post-mortem long-range

• 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

• Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.

  heart degs gene genes bulk gene kegg

• 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

• Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

  PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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  Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

  abc hek293 expressing sophie computational transporter transport

• The future is genome-wide.

  PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

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  Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

  schizophrenia myocardial individuals infectious genetic candidate gene

• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

  PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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  There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

  genomic pcr large outbred comparative denaturing pcr

• Targeted capture and massively parallel sequencing of 12 human exomes.

  PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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  Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

  hapmap unrelated na18507 randomly targeted array-based molecular

• Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

  PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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  Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

  peripheral population-based same germline epidemiological genotype-phenotype

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• Discovering the phylodynamics of RNA viruses.

  PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

  h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome