From: Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry
Application type | Description | Citation | Computational approach |
---|---|---|---|
Control of HIV infection | Protein function study of HIV restriction properties in TRIM5α | [40] | Codon model tests for selection |
Model species selection for pharmaceutical discovery | Assessment of pharmacological target homology | [42] | Phylogenetic analyses of gene families |
HIV vaccine development | Assessment of phylogenetic diversity in viral proteins and antibodies; identification of conserved epitopes | Phylogenetic analyses and codon model tests for selection | |
Flu epidemics prediction; vaccine strain selection | Modeling of antigenic dynamics of flu over time | [54] | Phylogenetic diffusion model of antigenic evolution |
Prediction of HIV progression | Monitoring the synonymous substitution rates in viral protein samples from HIV-positive patients over time | [67] | “Relaxed-clock” modeling of codon evolution |
Evaluating epidemics dynamics and the effect of public health interventions | Estimating the rates of transmission, recovery, sampling, and the effective reproductive number | Birth-death phylogenetic models | |
Flu epidemics prediction; vaccine strain selection | Modeling adaptive epitope changes and deleterious mutations outside the epitopes in flu from one year to the next | [93] | Molecular evolution modeling over viral genealogies |
Crop resistance | Identifying the resistant variants of the Pi-ta gene in rice that is used to control rice blast disease | [96] | Analyses of genetic diversity and evolution |
Mapping disease associations; complex disease biology; development personalized medicine | Genome studies identifying sites of genomic diversification, associations with diseases, estimating fitness of mutations | Evolutionary analyses of genomic constraints, genome-wide association studies | |
*Disease biology; identification of vaccine targets | Population genomics of the sexually transmitted bacteria Chlamydia trachomatis | [97] | Genome-wide evolutionary analyses of conservation by codon models and population genetics approaches |
*Disease biology | Adaptation in the cavity causing bacteria Streptococcus mutans | [98] | Genome-wide evolutionary analyses of conservation and demography |
*Conservation and biodiversity; climate change | Evaluating hybridization of blue whale subspecies in southern hemisphere | [99] | Population genetics analyses |
*Impact of climate change | Evaluating the interplay between global climate change, genetic diversity and species interactions and community structure | [100] | Evaluation of intraspecific genetic diversity by population genetics approaches |