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).

• Identifying the important HIV-1 recombination breakpoints.

  PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

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  Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

  inter-subtype parental copy-choice probabilistic comparative

• Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

  PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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  Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

  gp41 hiv-1 recombination site-specific comparative

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  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

• HIV-1 sequence evolution in vivo after superinfection with three viral strains.

  PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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  gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

  blood seminal pbmcs biological strain-specific bulk in-house

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• High genetic variability of HIV-1 in female sex workers from Argentina.

  PMID 17697319 · PMC1971708 · Retrovirology · 2007 · 7 claims · 6 setups

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  HIV-1 genetic diversity among Argentine FSWs is extensive, with BF recombinants predominating over subtypes B and C

  pbmc-derived aligned near pro heteroduplex pcr near

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil.

  PMID 10081673 · PMC2627691 · Emerging infectious diseases · 1999 · 8 claims · 8 setups

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  Among 79 HIV-1 infected patients, 3 (3.8%) had dual infections, 6 (7.6%) had recombinant infections, and 70 (88.6%) had single-subtype infections

  pbmc uncultured pcr-amplified aligned rflp heteroduplex nested

• Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

  PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups

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  CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.

  pbmcs autologous vaccinia plasma ifn-γ 51cr recombinant

• First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

  PMID 16959032 · PMC1570496 · Retrovirology · 2006 · 8 claims · 6 setups

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  Nearly full-length sequencing of 10 HIV-1 seroincident MSM samples revealed 6 subtype B, 3 unique BF recombinants, and 1 novel B/C/F triple recombinant

  pbmcs assembled hiv-1 triple nearly phylogenetic bootscan

• New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

  PMID 18673538 · PMC2553414 · Retrovirology · 2008 · 7 claims · 5 setups

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  04FR-KZS clusters with two previously described DRC viruses and represents CRF27_cpx, a complex recombinant involving A/E/G/H/J/K/U subtypes.

  pbmcs v3-v5 full-length undetermined v3-v5 full-length phylogenetic