Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors
Publication Date
December 06, 2011
Journal
PLOS ONE
Authors
Raffaella Burioni, Riccardo Scalco & Mario Casartelli
Volume
6
Issue
12
Pages
e27924
DOI
https://dx.plos.org/10.1371/journal.pone.0027924
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0027924
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22162994
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232212
Europe PMC
http://europepmc.org/abstract/MED/22162994
Scopus
82755165113
Mendeley
http://www.mendeley.com/research/rohlin-distance-evolution-influenza-virus-weak-attractors-precursors
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Mendeley 1605 May 09:08 UTC

Mendeley | Further Information

{"title"=>"Rohlin distance and the evolution of influenza a virus: Weak attractors and precursors", "type"=>"journal", "authors"=>[{"first_name"=>"Raffaella", "last_name"=>"Burioni", "scopus_author_id"=>"7004828274"}, {"first_name"=>"Riccardo", "last_name"=>"Scalco", "scopus_author_id"=>"52164356700"}, {"first_name"=>"Mario", "last_name"=>"Casartelli", "scopus_author_id"=>"6701376607"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-82755165113", "pmid"=>"22162994", "doi"=>"10.1371/journal.pone.0027924", "pui"=>"363035558", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "arxiv"=>"arXiv:1112.2608v1", "sgr"=>"82755165113"}, "id"=>"2eb3e122-d5cd-3091-b283-2ec060277cf8", "abstract"=>"The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about the sequences and it is sensitive to the correlated variations in the characters disposition. Its efficiency is improved by algorithmic tools, designed to enhance the detection of the novelty and to reduce the noise of useless mutations. We focus on the USA data from 1993/94 to 2010/2011 for A/H3N2 and on USA data from 2006/07 to 2010/2011 for A/H1N1. We show that the clusterization of the distance matrix gives strong evidence to a structure of domains in the sequence space, acting as weak attractors for the evolution, in very good agreement with the epidemiological history of the virus. The structure proves very robust with respect to the variations of the clusterization parameters, and extremely coherent when restricting the observation window. The results suggest an efficient strategy in the vaccine forecast, based on the presence of \"precursors\" (or \"buds\") populating the most recent attractor.", "link"=>"http://www.mendeley.com/research/rohlin-distance-evolution-influenza-virus-weak-attractors-precursors", "reader_count"=>16, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Materials Science"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>0}
Scopus 105 Sep 23:11 UTC

Scopus | Further Information

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Figshare 1102 Apr 21:00 UTC

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/705517"], "description"=>"<p>Rohlin analysis during years. Clusters structure is robust under a sampling increase, and buds appeared during seasons correctly reveal the future circulating strains, as indicated by the syringe.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>375880, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changing_the_time_window_/375880", "title"=>"Changing the time window.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-06 01:38:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/705290"], "description"=>"<p>(upper part) Rohlin clusters time evolution for H3N2. (lower part) Hamming clusters time evolution for H3N2. The reference WHO sequences are shown by the corresponding symbols and names, and the details are indicated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027924#pone-0027924-t001\" target=\"_blank\">Table 1</a>. In the upper part, we indicate the vaccine choice according to the WHO indication (up) and to buds criterion (lower). Green and red colors indicate right and wrong choice with respect to the corresponding analysis on the real circulating strain. A double color is used when more than one strain circulated in that year and the corresponding prediction agrees with one of the circulating strain.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>375654, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clusters_and_time_evolution_for_H3N2_/375654", "title"=>"Clusters and time evolution for H3N2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-06 01:34:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/358124", "https://ndownloader.figshare.com/files/358147", "https://ndownloader.figshare.com/files/358189", "https://ndownloader.figshare.com/files/358220"], "description"=>"<div><p>The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about the sequences and it is sensitive to the correlated variations in the characters disposition. Its efficiency is improved by algorithmic tools, designed to enhance the detection of the novelty and to reduce the noise of useless mutations. We focus on the USA data from 1993/94 to 2010/2011 for A/H3N2 and on USA data from 2006/07 to 2010/2011 for A/H1N1. We show that the clusterization of the distance matrix gives strong evidence to a structure of domains in the sequence space, acting as weak attractors for the evolution, in very good agreement with the epidemiological history of the virus. The structure proves very robust with respect to the variations of the clusterization parameters, and extremely coherent when restricting the observation window. The results suggest an efficient strategy in the vaccine forecast, based on the presence of “precursors” (or “buds”) populating the most recent attractor.</p> </div>", "links"=>[], "tags"=>["rohlin", "influenza", "attractors", "precursors"], "article_id"=>130787, "categories"=>["Cancer", "Biological Sciences", "Physics", "Biotechnology", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0027924.s001", "https://dx.doi.org/10.1371/journal.pone.0027924.s002", "https://dx.doi.org/10.1371/journal.pone.0027924.s003", "https://dx.doi.org/10.1371/journal.pone.0027924.s004"], "stats"=>{"downloads"=>6, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rohlin_Distance_and_the_Evolution_of_Influenza_A_Virus_Weak_Attractors_and_Precursors/130787", "title"=>"Rohlin Distance and the Evolution of Influenza A Virus: Weak Attractors and Precursors", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-06 00:13:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/705404"], "description"=>"<p>(upper part) Rohlin clusters time evolution for H1N1. (lower part) Hamming clusters time evolution for H1N1. The reference WHO sequences are shown by the corresponding symbols, as indicated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027924#pone-0027924-t002\" target=\"_blank\">Table 2</a>. In the upper part, we indicate the vaccine choice according to the WHO indication (up) and to buds criterion (lower). Green and red colors indicate right and wrong choice. In this case, some of the symbols does not correspond to a specific HI test, so they are indicated by a star and a pentagon. Notice the onset of the pandemic virus and the failure of the bud criterion after that line.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>375764, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clusters_and_time_evolution_for_H1N1_/375764", "title"=>"Clusters and time evolution for H1N1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-06 01:36:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/705726"], "description"=>"<p>Symbols legend for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027924#pone-0027924-g002\" target=\"_blank\">Fig. 2</a>.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>376088, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Symbols_legend_for_Fig_2_/376088", "title"=>"Symbols legend for Fig. 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-06 01:41:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/705210"], "description"=>"<p><b> in clustering.</b> Clustering entropy for Hamming and Rohlin distance at different values for H3N2. The plateau, in Rohlin, suggests an optimal and stable result for the clustering.</p>", "links"=>[], "tags"=>["optimal"], "article_id"=>375576, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Looking_for_optimal_/375576", "title"=>"Looking for optimal", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-06 01:32:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/705635"], "description"=>"<p>Two partitions and (derived from sequences as given in the text) and their maximal common factor . Thick vertical lines individuate the atomic segments. Below, the reduced partitions and . Colors in and remind the source configurations. There are no colors in , and because these partitions do not originate from sequences of symbols but are directly defined in the partition space.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>376001, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reduction_/376001", "title"=>"Reduction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-06 01:40:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/705763"], "description"=>"<p>Symbols legend for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027924#pone-0027924-g003\" target=\"_blank\">Fig. 3</a>.</p>", "links"=>[], "tags"=>["public health and epidemiology", "Infectious diseases", "Computational biology", "Evolutionary biology", "physics"], "article_id"=>376127, "categories"=>["Physics", "Biological Sciences", "Biotechnology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Raffaella Burioni", "Riccardo Scalco", "Mario Casartelli"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027924.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Symbols_legend_for_Fig_3_/376127", "title"=>"Symbols legend for Fig. 3.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-06 01:42:07"}
PMC Usage Stats 55517 Sep 15:42 UTC

PMC Usage Stats | Further Information

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Relative Metric 76261212 Apr 19:31 UTC

Relative Metric

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