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).
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Adaptation to different human populations by HIV-1 revealed by codon-based analyses.
PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups
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.
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HIV-1 sequence evolution in vivo after superinfection with three viral strains.
PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups
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
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Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups
A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.
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Has reproduction · 94
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.
PMID 35794110 · PMC9258765 · Nature communications · 2022 · 8 claims · 5 setups
Deep learning (FFNN-SS and CNN-CBLV) enables accurate and fast likelihood-free estimation of epidemiological parameters and model selection from phylogenies