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).

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.

  apis algerian ld-pruned reference whole-genome read identity-by-descent

• 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

• No evidence of a Neanderthal contribution to modern human diversity.

  PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

  Full-text index only

  There is no evidence of any Neanderthal contribution to modern human genetic diversity

  neanderthal culture modern genomic mitochondrial nuclear gene-specific

• 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

• Calculating expected DNA remnants from ancient founding events in human population genetics.

  PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

  Full-text index only

  Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

  simulated forward-based size

• SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

  PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

  Full-text index only

  SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

  sidcon real mixtures snp re-analysis

• 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