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).

• Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

  PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

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  Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

  hiv-1 same brazilian phylogenetic bootstrap pruning

• Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

  PMID 17300723 · PMC1805740 · Virology journal · 2007 · 7 claims · 7 setups

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  Genetic distance and heterogeneity between HCV quasispecies is a critical predictor of IFN response in Egyptian genotype-4 patients

  serum pcr cloned 5'utr rt-pcr molecular sequencing

• Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression.

  PMID 18769357 · PMC3071283 · Journal of acquired immune deficiency syndromes (1999) · 2008 · 7 claims · 6 setups

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  HIV coinfection is associated with ~0.5 log10 higher HCV RNA levels, suggesting increased HCV replication

  chronically paired aligned hiv-infected direct genetic sliding-window

• Needles in the haystack: identifying individuals present in pooled genomic data.

  PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

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  The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

  cgems hapmap genetic-distance within-population snp-count

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical

• 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

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  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

• Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

  PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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  14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

  h3n2 meme sequence entropy

• Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

  PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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  The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

  genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise

• Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

  PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  Dutch traditional chicken breeds show a complex and admixed subdivided population structure that partly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

  chickens dutch individuals phased whole-genome principal neighbor-joining

• Global distribution of rubella virus genotypes.

  PMID 14720390 · PMC3034328 · Emerging infectious diseases · 2003 · 8 claims · 6 setups

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  Phylogenetic analysis of 103 E1 gene sequences from 17 countries confirms at least two rubella virus genotypes, RGI and RGII

  rubella same phylogenetic genetic virus

• The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

  PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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  Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

  pbmcs clonal env deduced nested maximum-likelihood positive

• Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

  PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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  Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

  serum hvr1 svr rt-pcr shannon hamming

• Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

  PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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  O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

  serum hbv full-length o-hbv nested phylogenetic quasispecies

• Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

  PMID 19772609 · PMC2759955 · BMC genetics · 2009 · 8 claims · 5 setups

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  Saudi Arabia differs from other Arabian Peninsula countries by a significantly higher presence of J2-M172 lineages.

  saudi same j1-m267 y-chromosome y-str amova

• Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

  PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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  Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

  prehispanic indigenous ancient modern y-chromosome nested real-time

• The effect of 16S rRNA region choice on bacterial community metabarcoding results.

  PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 8 setups

  Has reproduction · 59

  The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, enabling more precise distance-based OTU clustering.

  bacterial extracted filtered combined 16s pcr extraction

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 8 setups

  Has reproduction · 80

  After ~2 decades of ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin, especially centromeric/peri-centromeric satellite and micro-satellite DNA

  pbmc single cd4 pbmc-derived flip-seq mip-seq prip-seq

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome