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).

• Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

  PMID 36882868 · PMC9991879 · BMC medicine · 2023 · 8 claims · 6 setups

  Has reproduction · 89

  Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes

  population-level age-structured same ethiopia dynamic epidemiological daly

• 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

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• 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 evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees.

  PMID 31932598 · PMC6957680 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 93

  E. dilemma and E. viridissima are reproductively isolated genetically distinct lineages despite low genome-wide differentiation.

  orchid males dilemma or41 snp whole-genome gas

• In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

  PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups

  Full-text index only

  The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India

  mtdna mitochondrial partial hvs1

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

  Full-text index only

  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• 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

• Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

  PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 89

  Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.

  coli st372 core draft whole-genome core population

• Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

  PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

  Full-text index only

  N. lactamica por is less diverse than meningococcal porB2 and porB3

  lactamica unique pcr distance-based population

• Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

  PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

  Full-text index only

  The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

  isolates genome snp snps multilocus genome bayesian

• Candidates for Balancing Selection in Leishmania donovani Complex Parasites.

  PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups

  Has reproduction · 64

  Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)

  infantum donovani snp populations whole-genome read admixture

• Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

  PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

  blood charlesbogerti reptile annotated whole-genome novo repeat

• Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

  PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

  angora domesticated candidate low-coverage multivariate principal

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Microsatellites and SNPs linkage analysis in a Sardinian genetic isolate confirms several essential hypertension loci previously identified in different populations.

  PMID 19715579 · PMC2741446 · BMC medical genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  Three loci (2q24, 11q23.1-25, 13q14.11-21.33) were identified by both the microsatellite and SNP genome-wide scans

  talana volunteers same ogliastra genome-wide clinical genotype

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate