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).

• Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

  PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

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  PITX1 polymorphisms and haplotypes are significantly associated with autism

  agre pitx1 parental family-based extended haplotype

• PDA: Pooled DNA analyzer.

  PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

  Full-text index only

  No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

  heterozygous pools ordered peak pooled single-point

• Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

  PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

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  None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

  genomic case-control nramp1 type sanger snp microsatellite

• A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis.

  PMID 18667089 · PMC2533022 · BMC genomics · 2008 · 7 claims · 2 setups

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  HFCC is a method/software for genome-wide epistasis detection using case-control multi-locus association analysis, combining a fast computing algorithm with flexibility to test a variety of epistatic models.

  blood-derived simulated genome-wide simulation-based

• Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

  PMID 18768181 · PMC2699582 · Atherosclerosis · 2009 · 8 claims · 6 setups

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  COX-2 promoter SNP rs689466 is associated with lower coronary calcified plaque (CorCP)

  whole-blood-derived subjects dhs unrelated snp coronary carotid

• Genome-wide associations of aortic distensibility suggest causality for aortic aneurysms and brain white matter hyperintensities.

  PMID 35922433 · PMC9349177 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction

  Genome-wide association of six CMR-derived aortic traits in up to 32,590 UK Biobank participants identifies 102 loci (including 27 novel associations) for aortic distensibility and area.

  biobank arterial aortic genome-wide multi-trait cardiac

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction

  Discovery and replication GWAS of SBP, DBP and pulse pressure in up to 776,078 individuals identified 208 novel common blood pressure SNPs and 53 rare variants.

  mvp tissues kidney gwas genome-wide transcriptome-wide

• The brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism and depression in Mexican-Americans.

  PMID 17632285 · PMC2686836 · Neuroreport · 2007 · 7 claims · 4 setups

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  BDNF SNP rs6265 (Val66Met) is significantly associated with diagnosis of major depression in Mexican-Americans

  genomic same participants genotyped snp hardy-weinberg clinical

• Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.

  PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 6 claims · 8 setups

  Has reproduction · 69

  Meta-analysis of GWAS across multiple breeds for CM and SCS identified 58 lead markers associated with mastitis incidence, including 16 loci not overlapping previously identified QTL in AnimalQTLdb.

  six multi-breed per-breed bovine genome-wide single-trait trans-ethnic

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic

• Imputation-based analysis of association studies: candidate regions and quantitative traits.

  PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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  Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

  study phenotyped genotype bayesian

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Association of GSK3B with Alzheimer disease and frontotemporal dementia.

  PMID 18852354 · PMC2841136 · Archives of neurology · 2008 · 8 claims · 5 setups

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  The GSK3B intronic polymorphism IVS2-68G>A is associated with increased risk of AD and FTD in a case-control cohort

  genomic case-control family-based sib-pair pcr allele-specific fluorescence-polarization

• Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

  PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

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  Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

  eye genomic tnnt1 cdna genomic snp

• 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

• Urinary proteomic profiling for diagnostic bladder cancer biomarkers.

  PMID 19811072 · PMC3422861 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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  Single protein biomarkers (e.g., NMP-22, BTA) suffer from high false-positive rates and none have replaced cystoscopy or cytology for bladder cancer detection.

  urine page gel 2d-dige