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).

• Topological approximate Bayesian computation for parameter inference of an angiogenesis model.

  PMID 35191485 · PMC9048691 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 3 setups

  Has reproduction · 100

  TDA summary statistics can be combined with ABC to infer parameters (ρ, χ) of the Anderson–Chaplain angiogenesis model

  square simplicial simulated computational persistent approximate

• Quantitative analysis of single nucleotide polymorphisms within copy number variation.

  PMID 19093001 · PMC2600609 · PloS one · 2008 · 8 claims · 2 setups

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  Copy number variation is a major factor in HWE violation for SNPs with small minor allele frequency, large sample size, and 0-1% genotyping error rate

  biallelic simulated bayesian chi-square

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• PDA: Pooled DNA analyzer.

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

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  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

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

  PMID 19888473 · PMC2768585 · PLoS computational biology · 2009 · 8 claims · 5 setups

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  Translocation-related human proteins are significantly enriched in intrinsic structural disorder compared to all human proteins

  translocation-related translocation cyclin-dependent intrinsic pfam randomized

• Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

  PMID 19888326 · PMC2765618 · PloS one · 2009 · 7 claims · 4 setups

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  The frequency of SAA1 alpha/alpha homozygotes is much higher among Armenian FMF patients (24%) than Karabakhian FMF patients (4%)

  genomic population simulated pcr pearson monte

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• The (CTG)n polymorphism in the NOTCH4 gene is not associated with schizophrenia in Japanese individuals.

  PMID 11407996 · PMC32311 · BMC psychiatry · 2001 · 6 claims · 4 setups

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  No significant differences in genotype or allele frequencies of the NOTCH4 (CTG)n repeat were found between schizophrenia patients and controls

  genomic pcr genotype pcr-based direct pcr

• SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

  PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.

  african simulated hardy-weinberg haplotype linkage