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).

• SNP-VISTA: an interactive SNP visualization tool.

  PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets

  abo homologous acid snp multi-species blast-based

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Absence of the TAP2 human recombination hotspot in chimpanzees.

  PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

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  The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

  western haplotype males simulated resequencing ld-based sperm

• Recombination events restored the functional horned haplotypes in the offspring of polled parents.

  PMID 41174470 · PMC12579413 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 7 setups

  Has reproduction · 98

  In the Holstein-Friesian (HF) trio, the horned offspring arose from non-allelic homologous recombination in the gametes of the P_F/P_F sire.

  trio fleckvieh whole-genome snp pcr-based

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

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

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

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  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

• Evolutionary algorithms for the selection of single nucleotide polymorphisms.

  PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).

  simulated mhc evolutionary multiobjective

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• Simple models of genomic variation in human SNP density.

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

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  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

• A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

  PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups

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  A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes

  hapmap 5-snp genome-wide first maximum mutual pearson

• Inferring human colonization history using a copying model.

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

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  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

• Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

  PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

  Has reproduction · 51

  K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

  uniflora whole-genome phylogenomic population

• The EPHA2 gene is associated with cataracts linked to chromosome 1p.

  PMID 19005574 · PMC2582197 · Molecular vision · 2008 · 5 claims · 5 setups

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  A heterozygous c.2842G>T (p.G948W) mutation in EPHA2 exon 17 causes autosomal dominant posterior polar cataracts in family Mu

  family case-control genome-wide str pcr

• Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

  PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

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  A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

  bovis bcg genomic cell-free allelic southern sequencing

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

  PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

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  SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

  african-american thai same study sanger snp genotyping

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups

  Has reproduction · 82

  Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

  klebsiella isolate a55848 assembled short-read phenotypic genome-based