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).

• Modeling the amplification dynamics of human Alu retrotransposons.

  PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

  Full-text index only

  Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

  simulated genome population computer comparative population

• Analysis of concordance of different haplotype block partitioning algorithms.

  PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups

  Full-text index only

  Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.

  simulated subsamples coalescent diversity-based ld-based

• Inferring human colonization history using a copying model.

  PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

  simulated populations coalescent snp ascertainment

• Stability analysis of mixtures of mutagenetic trees.

  PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

  Full-text index only

  Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

  simulated hiv-1 hiv timed simulation genotypic mutagenetic

• Sex-biased evolutionary forces shape genomic patterns of human diversity.

  PMID 18818765 · PMC2538571 · PLoS genetics · 2008 · 7 claims · 5 setups

  Full-text index only

  X-linked diversity is higher than the neutral expectation (0.75) relative to autosomal diversity in all six sampled human populations

  humans population simulated computational resequencing coalescent-based coalescent

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

  Full-text index only

  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

  PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

  Has reproduction · 68

  200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

  african lion crater simulated genome principal admixture

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

  Full-text index only

  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• 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