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).

• Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

  PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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  Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

  hiv-1 polyclonally shannon cross-clade ctl

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• 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

• Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

  PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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  Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

  genbank hiv-1 protease integrase blastp phylogenetic amino

• 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

• 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

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

  microbial quality-filtered overflowing shotgun taxonomic alpha

• SARS-CoV genome polymorphism: a bioinformatics study.

  PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

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  SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

  sars-cov annotated spike whole-genome positional codon

• 'Genome design' model and multicellular complexity: golden middle.

  PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

  normal genes proteins encoded oligonucleotide gene functional