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).

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• 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

• HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

  PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

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  Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

  plasma transmitter subject genomic full-length population ifn-γ

• 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 high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

  PMID 17997604 · PMC2065879 · PLoS pathogens · 2007 · 8 claims · 5 setups

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  Two enJSRV proviruses (enJS56A1 and enJSRV-20) independently acquired a defective, transdominant Gag (R21W substitution) that blocks late replication steps of exogenous JSRV/ENTV

  sheep nih3t3 domestic enjsrv bac retroviral locus-specific

• Emergence of recombinant forms of HIV: dynamics and scaling.

  PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

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  A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

  cd4+ scid-hu splenocytes computational single-round replication-competent proviral

• 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

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter