Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution.
Human Immunodeficiency Virus type 1 (HIV-1) because of high mutation rates, large population sizes, and rapid replication, exhibits complex evolutionary strategies. For the analysis of evolutionary processes, the graphical representation of fitness landscapes provides a significant advantage. The ex...
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0088579&type=printable |
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| author | Ramón Lorenzo-Redondo Soledad Delgado Federico Morán Cecilio Lopez-Galindez |
| author_facet | Ramón Lorenzo-Redondo Soledad Delgado Federico Morán Cecilio Lopez-Galindez |
| author_sort | Ramón Lorenzo-Redondo |
| collection | DOAJ |
| description | Human Immunodeficiency Virus type 1 (HIV-1) because of high mutation rates, large population sizes, and rapid replication, exhibits complex evolutionary strategies. For the analysis of evolutionary processes, the graphical representation of fitness landscapes provides a significant advantage. The experimental determination of viral fitness remains, in general, difficult and consequently most published fitness landscapes have been artificial, theoretical or estimated. Self-Organizing Maps (SOM) are a class of Artificial Neural Network (ANN) for the generation of topological ordered maps. Here, three-dimensional (3D) data driven fitness landscapes, derived from a collection of sequences from HIV-1 viruses after "in vitro" passages and labelled with the corresponding experimental fitness values, were created by SOM. These maps were used for the visualization and study of the evolutionary process of HIV-1 "in vitro" fitness recovery, by directly relating fitness values with viral sequences. In addition to the representation of the sequence space search carried out by the viruses, these landscapes could also be applied for the analysis of related variants like members of viral quasiespecies. SOM maps permit the visualization of the complex evolutionary pathways in HIV-1 fitness recovery. SOM fitness landscapes have an enormous potential for the study of evolution in related viruses of "in vitro" works or from "in vivo" clinical studies with human, animal or plant viral infections. |
| format | Article |
| id | doaj-art-6a2ed8afb4a841e8b4de71a78d165cf0 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-6a2ed8afb4a841e8b4de71a78d165cf02025-08-20T03:01:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0192e8857910.1371/journal.pone.0088579Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution.Ramón Lorenzo-RedondoSoledad DelgadoFederico MoránCecilio Lopez-GalindezHuman Immunodeficiency Virus type 1 (HIV-1) because of high mutation rates, large population sizes, and rapid replication, exhibits complex evolutionary strategies. For the analysis of evolutionary processes, the graphical representation of fitness landscapes provides a significant advantage. The experimental determination of viral fitness remains, in general, difficult and consequently most published fitness landscapes have been artificial, theoretical or estimated. Self-Organizing Maps (SOM) are a class of Artificial Neural Network (ANN) for the generation of topological ordered maps. Here, three-dimensional (3D) data driven fitness landscapes, derived from a collection of sequences from HIV-1 viruses after "in vitro" passages and labelled with the corresponding experimental fitness values, were created by SOM. These maps were used for the visualization and study of the evolutionary process of HIV-1 "in vitro" fitness recovery, by directly relating fitness values with viral sequences. In addition to the representation of the sequence space search carried out by the viruses, these landscapes could also be applied for the analysis of related variants like members of viral quasiespecies. SOM maps permit the visualization of the complex evolutionary pathways in HIV-1 fitness recovery. SOM fitness landscapes have an enormous potential for the study of evolution in related viruses of "in vitro" works or from "in vivo" clinical studies with human, animal or plant viral infections.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0088579&type=printable |
| spellingShingle | Ramón Lorenzo-Redondo Soledad Delgado Federico Morán Cecilio Lopez-Galindez Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. PLoS ONE |
| title | Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. |
| title_full | Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. |
| title_fullStr | Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. |
| title_full_unstemmed | Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. |
| title_short | Realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental HIV-1 evolution. |
| title_sort | realistic three dimensional fitness landscapes generated by self organizing maps for the analysis of experimental hiv 1 evolution |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0088579&type=printable |
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