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).

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

  PMID 35338232 · PMC8956664 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  Two computational approaches (sub-sampling and phenotype-simulation) can be implemented to perform power calculations for bacterial GWAS using existing genome collections, packaged as the PowerBacGWAS pipeline

  enterococcus klebsiella mycobacterium faecium pan-genome burden variant

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• 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

• Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.

  PMID 29187638 · PMC5721160 · Journal of the Royal Society, Interface · 2017 · 7 claims · 8 setups

  Has reproduction · 49

  Numb (and Numbl) inhibits a full EMT by stabilizing a hybrid E/M phenotype, acting as a 'phenotypic stability factor'.

  notch-emt-numb h1975 independent mathematical multi-cell sirna

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.

  PMID 18567820 · PMC2518507 · Diabetes · 2008 · 8 claims · 5 setups

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  CDC123/CAMK1D rs12779790 risk allele (homozygous) is associated with decreased insulinogenic index, corrected insulin response (CIR), and AUC-insulin/AUC-glucose ratio, indicating impaired insulin release

  inter99 same taqman oral general