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).

• BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

  PMID 15757512 · PMC555852 · Retrovirology · 2005 · 8 claims · 3 setups

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  BioAfrica's HIV-1 Proteomics Resource integrates protein structure, gene expression, post-translational modification, functional activity and protein-macromolecule interaction data with bioinformatics tools in a single website.

  hiv-1 motif sequence literature-derived

• Wiggle-predicting functionally flexible regions from primary sequence.

  PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

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  A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

  hiv bovine calmodulin nonredundant gaussian gnm support

• 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

• 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

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Efficient algorithms for probing the RNA mutation landscape.

  PMID 18688270 · PMC2475669 · PLoS computational biology · 2008 · 8 claims · 4 setups

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  RNAmutants generalizes McCaskill's partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all k-point mutants, simultaneously computing MFE(k) and Z(k) for each k

  element hepatitis hiv utr partition deleterious mutation

• 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

• Structural genomics: a new era for pharmaceutical research.

  PMID 11864367 · PMC139010 · Genome biology · 2002 · 8 claims · 6 setups

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  Automation of crystal mounting, diffraction data collection, and structure determination/refinement is a critical factor enabling large-scale structural genomics projects.

  proteins target hiv x-ray thermal initio

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters.

  PMID 11897022 · PMC139022 · Genome biology · 2002 · 8 claims · 8 setups

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  Trans-splicing generates cell-specific protocadherin mRNAs in human neurons

  individual cancer pre-b saccharomyces reverse-transcriptase karyotypic spectral

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

  PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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  Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

  neisseria streptococcus coli vibrio reverse pan-genomic comparative