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).

• 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

• Direct maximum parsimony phylogeny reconstruction from genotype data.

  PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

  Full-text index only

  The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

  simulated mitochondrial lipoprotein coalescent maximum sliding-window

• The origins of lactase persistence in Europe.

  PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

  Full-text index only

  The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

  simulated simulation 910*t farming demic approximate comparison

• ADZE: a rarefaction approach for counting alleles private to combinations of populations.

  PMID 18779233 · PMC2732282 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 2 setups

  Full-text index only

  A generalized rarefaction-based statistic can estimate the sample size-corrected number of distinct alleles private to any combination of populations, generalizing Kalinowski's (2004) private allelic richness to groups of populations.

  populations simulated microsatellite computational

• LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.

  PMID 38877886 · PMC11179121 · Briefings in bioinformatics · 2024 · 6 claims · 2 setups

  Has reproduction · 90

  LoRA-TV jointly processes read-depth profiles of all cells by stacking them into a matrix and applying low-rank approximation plus total-variation smoothing to capture shared genomic signatures for clustering.

  tumor simulated single-cell simulation

• 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

• Digital evolution.

  PMID 14551915 · PMC212697 · PLoS biology · 2003 · 7 claims · 5 setups

  Full-text index only

  Digital organisms (Avidians) evolved from simple self-replicators, through an unexpected transitional form, to complex performers of many logic functions, with the full genealogy traceable and no missing links.

  digital bacteria long-term digital test gene-expression

• 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

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

  PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 7 setups

  Has reproduction · 53

  Current effective population size for all four farmed fish populations is small (≤50 fish), potentially threatening breeding-programme sustainability

  turbot gilthead european common rad linkage computer

• 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

• GABRG1 and GABRA2 as independent predictors for alcoholism in two populations.

  PMID 18818659 · PMC2656604 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

  Full-text index only

  GABRG1 SNPs and haplotypes are significantly associated with alcohol use disorder (AUD) in both Finnish Caucasians and Plains American Indians

  finnish plains population hapmap snp haplotype ancestry

• Iterative pruning PCA improves resolution of highly structured populations.

  PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

  Full-text index only

  ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

  simulated hapmap cattle shriver's simulated snp comparative

• Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

  PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

  bxd simulated subset populations genome-wide simulation genotype-phenotype

• A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

  PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

  Full-text index only

  Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

  snp irish french fst-based microsatellite genome-wide

• Genome-wide scans for loci under selection in humans.

  PMID 16004726 · PMC3525256 · Human genomics · 2005 · 8 claims · 4 setups

  Full-text index only

  Natural selection and population demographic history both distort patterns of genetic variation relative to the standard neutral model, so single-locus tests cannot unambiguously distinguish selection from demography.

  african-american european-american populations simulated tajima's fst coalescent

• 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

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

  Full-text index only

  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

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

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

  Full-text index only

  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

• Collisionless relaxation of a disequilibrated current sheet and implications for bifurcated structures.

  PMID 34145266 · PMC8213726 · Nature communications · 2021 · 6 claims · 3 setups

  Has reproduction · 95

  Collisionless transitions among four single-particle orbit classes are responsible for the relaxation/equilibration of a disequilibrated current sheet.

  harris disequilibrated earth's single-particle particle-in-cell spacecraft