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).

• 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

• 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

• Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

  PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

  Full-text index only

  Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

  anopheles mtdna microsatellite population

• Updated three-stage model for the peopling of the Americas.

  PMID 18797500 · PMC2527656 · PloS one · 2008 · 8 claims · 3 setups

  Full-text index only

  Removing nine non-Native American mtDNA sequences eliminates the previously reported early (~40 kya) expansion signal for the proto-Amerind population

  native mitochondrial new bayesian mtdna molecular

• Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

  PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

  boars lwd lws pig whole-genome genetic genome-wide

• The formation of avian montane diversity across barriers and along elevational gradients.

  PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.

  forest population individuals single whole-genome f_st principal

• 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

• Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

  PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

  mandenka worldwide hapmap nat2 full snp 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

• Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

  PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

  newly duck southeast chinese whole-genome phylogenetic population

• 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

• 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

• Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

  PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

  Full-text index only

  Mutations in the OAZ3 gene are not a common cause of male infertility

  genomic coding inferred oaz3 direct sscp haplotype

• Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

  PMID 37160956 · PMC10169776 · Scientific reports · 2023 · 7 claims · 8 setups

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  Spontaneous ΦD5-resistant D. solani mutants DsR34 and DsR207 show significantly reduced virulence and colonization ability in planta compared to wild-type

  potato solani planta maceration genome

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

  PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.

  hapmap genotype genotype raw case-control

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

  PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

  Full-text index only

  Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

  simulated simulation-based simulated

• 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

• MSI test to distinguish between HNPCC and other predisposing syndromes -- of value in tailored surveillance.

  PMID 15528791 · PMC3839337 · Disease markers · 2004 · 8 claims · 5 setups

  Full-text index only

  MSI (or immunohistochemistry) testing applied to a pre-selected patient with a family history or early-onset colorectal cancer can distinguish HNPCC from unknown non-HNPCC colorectal cancer syndromes.

  population-based swedish colorectal hnpcc clinical histopathological microsatellite

• 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