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).

• Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

  PMID 19661472 · PMC2753702 · Stroke · 2009 · 8 claims · 6 setups

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  EDN SNP rs1800542 is associated with increased ischemic stroke risk in Caucasian women

  international spyw candidate haplotype population

• An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

  PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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  Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

  unrelated shanghai tsnps snp allele linkage

• Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

  PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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  IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

  population blood genomic hapmap snp survival allele

• 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

• Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

  PMID 19043545 · PMC2581785 · PLoS genetics · 2008 · 7 claims · 4 setups

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  A GWA study using serum metabolomics identifies SNPs associated with metabolite concentrations, explaining up to 12% of variance for single metabolites

  kora fasting genome-wide targeted metabolite

• Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

  PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

  hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• The detection of regions of our genome under selection has increasingly relied on the use of genome scans.

  PMID 16197732 · PMC3525123 · Human genomics · 2005 · 8 claims · 3 setups

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  Markers linked to a locus under local adaptation show larger variance in allele frequencies across populations (higher FST) than neutral markers

  populations common genome snp comparative

• 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

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

  PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

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  A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

  breast carcinogenesis-related nssnp-containing african gene snp functional

• Adaptations to climate in candidate genes for common metabolic disorders.

  PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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  A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

  individuals population genic compiled snp spearman bayesian

• SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

  PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools

  genome reference genomic runtime sequence comparative

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations.

  PMID 19715579 · PMC2741446 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  Three loci (2q24, 11q23.1-25, 13q14.11-21.33) were identified by both the microsatellite and SNP genome-wide scans

  talana volunteers same ogliastra genome-wide clinical genotype

• Evolution of genomic sequence inhomogeneity at mid-range scales.

  PMID 19891785 · PMC2779198 · BMC genomics · 2009 · 7 claims · 3 setups

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  MRI regions have comparable levels of de novo mutations to control genomic sequences with average base composition.

  chimpanzee population genome whole-genome snp indel

• Candidates for Balancing Selection in Leishmania donovani Complex Parasites.

  PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups

  Has reproduction · 64

  Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)

  infantum donovani snp populations whole-genome read admixture

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip