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).

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing

• HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

  PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

  Full-text index only

  HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

  t-cell identified gel maldi-tof bioinformatics

• Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance.

  PMID 19918099 · PMC4155129 · Antiviral therapy · 2009 · 8 claims · 6 setups

  Full-text index only

  Primary integrase inhibitor resistance mutations (T66I, E92Q, G140S, Y143C/H/R, Q148H/R/K, N155S/H) were absent in 342 drug-naive individuals, indicating these sites are highly constrained.

  plasma genomic viral aligned bulk sequence-based quantitative

• 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

  Full-text index only

  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

• Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

  PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

  Full-text index only

  Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

  cd4+ hela influenza-infected liver cdna microarray mass

• 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

  Full-text index only

  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

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

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

  Full-text index only

  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

• 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

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

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

  Full-text index only

  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

• Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

  PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

  Full-text index only

  IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

  saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

• Host-pathogen studies in the post-genomic era.

  PMID 11178231 · PMC138846 · Genome biology · 2000 · 7 claims · 7 setups

  Full-text index only

  DNA arrays have been used to study host and/or pathogen gene expression for four viruses (HCMV, HHV8, HIV-1, HPV31) and two bacteria (Listeria monocytogenes, Salmonella)

  foreskin b-cell t-cell normal pathogen host