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Grant support

Work in CNM is supported by grant SAF 2007-61036 and 2010-17226 from MINECO Spain, by grants 36558/06, 36641/07, 36779/08, 360766/09 from FIPSE Spain, and in part by the RETIC de Investigacion en SIDA (Red de grupos 173) of the Fondo de Investigaciones Sanitarias (FISss). Work in UCM is supported by grants BFU 2009-12895-C02-02 MICINN and BFU2012-39816-C02-02 from MINECO (Spain). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Delgado, SoledadAuthor
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Article

Realistic Three Dimensional Fitness Landscapes Generated by Self Organizing Maps for the Analysis of Experimental HIV-1 Evolution

Publicated to:Plos One. 9 (2): e88579- - 2014-02-28 9(2), DOI: 10.1371/journal.pone.0088579

Authors: Lorenzo-Redondo, Ramon; Delgado, Soledad; Moran, Federico; Lopez-Galindez, Cecilio;

Affiliations

Inst Salud Carlos III, Ctr Nacl Microbiol, Madrid, Spain - Author
Univ Complutense Madrid, Dept Bioquim & Biol Mol 1, Madrid, Spain - Author
Univ Politecn Madrid, Escuela Univ Informat, Dept Org & Estruct Informac, Madrid, Spain - Author

Abstract

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.

Keywords
AdaptationHiv infectionsHiv-1HumansImmunodeficiency-virus type-1In-vivo fitnessMutationNeural networks, computerOptimizationPhylogenyPopulation-dynamicsProteaseRecoveryRegionRna virus

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Plos One due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2014, it was in position 9/57, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 2.59, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-25, the following number of citations:

  • WoS: 8
  • Scopus: 13
  • OpenCitations: 16
Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-25:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 44.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 44 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 0.25.
  • The number of mentions on the social network X (formerly Twitter): 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United States of America.