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).

• A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

  PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

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  A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

  peripheral pedigree nuclear family snp two-point multipoint

• 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

• Sequence determinants of human microsatellite variability.

  PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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  Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

  hgdp-ceph genome calibrated microsatellite blastn sequence

• Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

  PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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  Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

  genomic pools training siddt individual pooled k-correction

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

  PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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  A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

  ebv-transformed serum combined rf-filtered snp serum random

• Weak or no association of TCF7L2 variants with Type 2 diabetes risk in an Arab population.

  PMID 18655717 · PMC2515290 · BMC medical genetics · 2008 · 8 claims · 4 setups

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  rs7903146 T allele frequency does not differ significantly between Saudi T2D cases and controls (OR 1.04, 95% CI 0.86-1.27, P=0.675)

  peripheral saudi genotype subset snp case-control haplotype

• 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

• 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

• Visualization of shared genomic regions and meiotic recombination in high-density SNP data.

  PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups

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  SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.

  trio family siblings synthetic snp synthetic mitochondrial

• Polymorphisms of delta-aminolevulinic acid dehydratase (ALAD) and peptide transporter 2 (PEPT2) genes in children with low-level lead exposure.

  PMID 19723536 · PMC2789866 · Neurotoxicology · 2009 · 7 claims · 3 setups

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  Children homozygous for the PEPT2*2 polymorphism have significantly higher blood lead levels than heterozygous or non-carrier children.

  mexican-american buccal parents blood genetic demographic

• High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

  PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups

  Has reproduction · 85

  SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.

  atlantic low-coverage genotyping genome

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

  PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

  msi-h aggregated genome mnr sigmoid genome-wide

• Addressing the obesity epidemic: a genomics perspective.

  PMID 17362622 · PMC1893129 · Preventing chronic disease · 2007 · 8 claims · 8 setups

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  Obesity is a multifactorial disorder reflecting complex interactions of genes, environment, and lifestyle

  identical fraternal children younger twin family longitudinal

• 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

• RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

  PMID 36429012 · PMC9688714 · Cells · 2022 · 6 claims · 7 setups

  Has reproduction · 37

  RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression.

  brain naïve wild-type spinal editing quantitative eae