Real Time Classification of Viruses in 12 Dimensions
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{"title"=>"Real Time Classification of Viruses in 12 Dimensions", "type"=>"journal", "authors"=>[{"first_name"=>"Chenglong", "last_name"=>"Yu", "scopus_author_id"=>"55487607100"}, {"first_name"=>"Troy", "last_name"=>"Hernandez", "scopus_author_id"=>"55744965300"}, {"first_name"=>"Hui", "last_name"=>"Zheng", "scopus_author_id"=>"55745036500"}, {"first_name"=>"Shek Chung", "last_name"=>"Yau", "scopus_author_id"=>"55557775800"}, {"first_name"=>"Hsin Hsiung", "last_name"=>"Huang", "scopus_author_id"=>"56563197900"}, {"first_name"=>"Rong Lucy", "last_name"=>"He", "scopus_author_id"=>"56040573300"}, {"first_name"=>"Jie", "last_name"=>"Yang", "scopus_author_id"=>"57192451929"}, {"first_name"=>"Stephen S.T.", "last_name"=>"Yau", "scopus_author_id"=>"57198033673"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84878082337", "pmid"=>"23717598", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84878082337", "issn"=>"19326203", "pui"=>"368973548", "doi"=>"10.1371/journal.pone.0064328"}, "id"=>"7c0fd4e0-5f2b-366a-aae0-520855d7b617", "abstract"=>"The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in [Formula: see text]. Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in [Formula: see text]. Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.", "link"=>"http://www.mendeley.com/research/real-time-classification-viruses-12-dimensions", "reader_count"=>33, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Student > Doctoral Student"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Computer Science"=>3, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Sweden"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1066615"], "description"=>"<div><p>The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in . Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in . Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.</p></div>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "microbiology", "Virology", "Viral classification", "Other viral groupings", "Viral genera unassigned to a family", "Viral evolution", "statistics", "Biostatistics", "Statistical methods", "classification", "viruses", "12"], "article_id"=>706282, "categories"=>["Mathematics", "Biological Sciences"], "users"=>["Chenglong Yu", "Troy Hernandez", "Hui Zheng", "Shek-Chung Yau", "Hsin-Hsiung Huang", "Rong Lucy He", "Jie Yang", "Stephen S.-T. Yau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064328", "stats"=>{"downloads"=>9, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Real_Time_Classification_of_Viruses_in_12_Dimensions_/706282", "title"=>"Real Time Classification of Viruses in 12 Dimensions", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-22 01:44:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1066607"], "description"=>"<p>The natural graphical representation for the 67 single-segment referenced viruses of Baltimore V.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "microbiology", "Virology", "Viral classification", "Other viral groupings", "Viral genera unassigned to a family", "Viral evolution", "statistics", "Biostatistics", "Statistical methods", "graphical", "67", "single-segment", "referenced", "viruses", "baltimore"], "article_id"=>706276, "categories"=>["Mathematics", "Biological Sciences"], "users"=>["Chenglong Yu", "Troy Hernandez", "Hui Zheng", "Shek-Chung Yau", "Hsin-Hsiung Huang", "Rong Lucy He", "Jie Yang", "Stephen S.-T. Yau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064328.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_natural_graphical_representation_for_the_67_single_segment_referenced_viruses_of_Baltimore_V_/706276", "title"=>"The natural graphical representation for the 67 single-segment referenced viruses of Baltimore V.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-22 01:44:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1066596"], "description"=>"<p>(A) From each element draw a directed line(s) to its closest element(s). (B) Combine the connected elements in (A) using directed lines, resulting in two connected graphs, graph 1 and graph 2. (C) The final graphical representation is obtained by connecting element A in graph1 and element G in graph2, based on the distance matrix in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064328#pone-0064328-t002\" target=\"_blank\">Table 2</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary modeling", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "microbiology", "Virology", "Viral classification", "Other viral groupings", "Viral genera unassigned to a family", "Viral evolution", "statistics", "Biostatistics", "Statistical methods", "graph", "matrix"], "article_id"=>706273, "categories"=>["Mathematics", "Biological Sciences"], "users"=>["Chenglong Yu", "Troy Hernandez", "Hui Zheng", "Shek-Chung Yau", "Hsin-Hsiung Huang", "Rong Lucy He", "Jie Yang", "Stephen S.-T. Yau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064328.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_graph_construction_process_of_a_distance_matrix_shown_in_Table_2_/706273", "title"=>"The graph construction process of a distance matrix shown in Table 2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-22 01:44:33"}

PMC Usage Stats | Further Information

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Relative Metric

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