{"id":"https://openalex.org/W2027969303","doi":"https://doi.org/10.1371/journal.pcbi.1003515","title":"Viral Quasispecies Assembly via Maximal Clique Enumeration","display_name":"Viral Quasispecies Assembly via Maximal Clique Enumeration","publication_year":2014,"publication_date":"2014-03-27","ids":{"openalex":"https://openalex.org/W2027969303","doi":"https://doi.org/10.1371/journal.pcbi.1003515","mag":"2027969303","pmid":"https://pubmed.ncbi.nlm.nih.gov/24675810"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003515","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003515","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003515&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003515&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060717574","display_name":"Armin T\u00f6pfer","orcid":"https://orcid.org/0000-0003-1637-1466"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Armin T\u00f6pfer","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067570776","display_name":"Tobias Marschall","orcid":"https://orcid.org/0000-0002-9376-1030"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Tobias Marschall","raw_affiliation_strings":["Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centrum Wiskunde & Informatica, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063994977","display_name":"Rowena A. Bull","orcid":"https://orcid.org/0000-0002-9844-3744"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Rowena A. Bull","raw_affiliation_strings":["Inflammation and Infection Research Centre, School of Medical Sciences, UNSW, Sydney, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inflammation and Infection Research Centre, School of Medical Sciences, UNSW, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002886777","display_name":"Fabio Luciani","orcid":"https://orcid.org/0000-0003-0666-6324"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Fabio Luciani","raw_affiliation_strings":["Inflammation and Infection Research Centre, School of Medical Sciences, UNSW, Sydney, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inflammation and Infection Research Centre, School of Medical Sciences, UNSW, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001148638","display_name":"Alexander Sch\u00f6nhuth","orcid":"https://orcid.org/0000-0003-3529-0856"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alexander Sch\u00f6nhuth","raw_affiliation_strings":["Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centrum Wiskunde & Informatica, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035497488","display_name":"Niko Beerenwinkel","orcid":"https://orcid.org/0000-0002-0573-6119"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Niko Beerenwinkel","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001148638","https://openalex.org/A5002886777","https://openalex.org/A5035497488","https://openalex.org/A5060717574","https://openalex.org/A5063994977","https://openalex.org/A5067570776"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1341640284","https://openalex.org/I31746571","https://openalex.org/I35440088"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":1841,"currency":"EUR","value_usd":1985},"fwci":5.6912,"has_fulltext":true,"cited_by_count":116,"citation_normalized_percentile":{"value":0.96877303,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"10","issue":"3","first_page":"e1003515","last_page":"e1003515"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.989799976348877,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/viral-quasispecies","display_name":"Viral quasispecies","score":0.9890008568763733},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.7476202249526978},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6352568864822388},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5661377310752869},{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.5534701347351074},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.49636274576187134},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44432106614112854},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.36069774627685547},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32247138023376465},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2801166772842407},{"id":"https://openalex.org/keywords/hepatitis-c-virus","display_name":"Hepatitis C virus","score":0.26563557982444763},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23426136374473572},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.18351387977600098},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1257844865322113},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11661791801452637}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.9890008568763733},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7476202249526978},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6352568864822388},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5661377310752869},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.5534701347351074},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49636274576187134},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44432106614112854},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.36069774627685547},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32247138023376465},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2801166772842407},{"id":"https://openalex.org/C2776408679","wikidata":"https://www.wikidata.org/wiki/Q708693","display_name":"Hepatitis C virus","level":3,"score":0.26563557982444763},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23426136374473572},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.18351387977600098},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1257844865322113},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11661791801452637},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D018414","descriptor_name":"CD8-Positive T-Lymphocytes","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1003515","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003515","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003515&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:24675810","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24675810","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:cwi:oai:cwi.nl:23964","is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/23964","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 10(3)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:2064e6e3f9d348efb334daaae6663cd3","is_oa":true,"landing_page_url":"https://doaj.org/article/2064e6e3f9d348efb334daaae6663cd3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 3, p e1003515 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2954209","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3967922","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/976785","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Viral_Quasispecies_Assembly_via_Maximal_Clique_Enumeration_/976785","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pub.uni-bielefeld.de:2941810","is_oa":false,"landing_page_url":"https://pub.uni-bielefeld.de/record/2941810","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"T\u00f6pfer A, Marschall T, Bull RA, Luciani F, Sch\u00f6nhuth A, Beerenwinkel N. Viral Quasispecies Assembly via Maximal Clique Enumeration. <em>PLoS Computational Biology</em>. 2014;10(3): e1003515.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3967922","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3967922","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/95957","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/95957","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 10 (3)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000095957","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000095957","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003515","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003515","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003515&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G312841952","display_name":"HIV-1 whole-genome quasispecies analysis in longitudinal clinical samples","funder_award_id":"146331","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7777748171","display_name":null,"funder_award_id":"639.072.039","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2027969303.pdf","grobid_xml":"https://content.openalex.org/works/W2027969303.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W820461064","https://openalex.org/W1565354039","https://openalex.org/W1567562836","https://openalex.org/W1970148090","https://openalex.org/W1975442866","https://openalex.org/W1982494640","https://openalex.org/W1992442812","https://openalex.org/W1993577356","https://openalex.org/W2003574450","https://openalex.org/W2003910843","https://openalex.org/W2006046315","https://openalex.org/W2010880827","https://openalex.org/W2012069101","https://openalex.org/W2013568176","https://openalex.org/W2022986961","https://openalex.org/W2023918737","https://openalex.org/W2027969303","https://openalex.org/W2037809979","https://openalex.org/W2047516879","https://openalex.org/W2049881004","https://openalex.org/W2051453551","https://openalex.org/W2065256070","https://openalex.org/W2073918065","https://openalex.org/W2094537279","https://openalex.org/W2095680943","https://openalex.org/W2106308757","https://openalex.org/W2107564978","https://openalex.org/W2107830007","https://openalex.org/W2118395479","https://openalex.org/W2126492433","https://openalex.org/W2127768708","https://openalex.org/W2134007392","https://openalex.org/W2135361281","https://openalex.org/W2148686896","https://openalex.org/W2151265018","https://openalex.org/W2153737961","https://openalex.org/W2160853127","https://openalex.org/W2160969485","https://openalex.org/W2163314170","https://openalex.org/W2163326395","https://openalex.org/W2163549019","https://openalex.org/W2164971951","https://openalex.org/W2170765088","https://openalex.org/W2401610261","https://openalex.org/W2571329707","https://openalex.org/W2951702327","https://openalex.org/W4211158349","https://openalex.org/W4230982365"],"related_works":["https://openalex.org/W2370565492","https://openalex.org/W2016766059","https://openalex.org/W2029741357","https://openalex.org/W108845024","https://openalex.org/W2144907742","https://openalex.org/W1748700469","https://openalex.org/W2009366069","https://openalex.org/W2620872782","https://openalex.org/W2086431635","https://openalex.org/W4253376477"],"abstract_inverted_index":{"Virus":[0],"populations":[1],"can":[2,125],"display":[3],"high":[4],"genetic":[5],"diversity":[6],"within":[7],"individual":[8],"hosts.":[9],"The":[10,91],"intra-host":[11],"collection":[12],"of":[13,23,39,52,83,93,157,166,186,193],"viral":[14,17,41],"haplotypes,":[15],"called":[16],"quasispecies,":[18],"is":[19,98,180],"an":[20,71,158],"important":[21],"determinant":[22],"virulence,":[24],"pathogenesis,":[25],"and":[26,68,107,134,138,161],"treatment":[27],"outcome.":[28],"We":[29,56,143],"present":[30],"HaploClique,":[31],"a":[32,40,58,151,163],"computational":[33],"approach":[34],"to":[35,112,119,146],"reconstruct":[36,126],"the":[37,191,194],"structure":[38],"quasispecies":[42,95],"from":[43,49,130,150],"next-generation":[44],"sequencing":[45,51,108,147,177],"data":[46,102,148],"as":[47],"obtained":[48],"bulk":[50],"mixed":[53],"virus":[54,155],"samples.":[55],"develop":[57],"statistical":[59],"model":[60],"for":[61,65,103],"paired-end":[62,114],"reads":[63],"accounting":[64],"mutations,":[66],"insertions,":[67],"deletions.":[69],"Using":[70],"iterative":[72],"maximal":[73],"clique":[74],"enumeration":[75],"approach,":[76],"read":[77],"pairs":[78],"are":[79],"assembled":[80],"into":[81],"haplotypes":[82,129],"increasing":[84],"length,":[85],"eventually":[86],"enabling":[87],"global":[88],"haplotype":[89,121],"assembly.":[90],"performance":[92],"our":[94],"assembly":[96],"method":[97],"assessed":[99],"on":[100],"simulated":[101],"varying":[104],"population":[105,156],"characteristics":[106],"technology":[109],"parameters.":[110],"Owing":[111],"its":[113],"handling,":[115],"HaploClique":[116,145,179],"compares":[117],"favorably":[118],"state-of-the-art":[120],"inference":[122],"methods.":[123],"It":[124],"error-free":[127],"full-length":[128],"low":[131,141],"coverage":[132],"samples":[133],"detect":[135],"large":[136],"insertions":[137],"deletions":[139],"at":[140,182],"frequencies.":[142],"applied":[144],"derived":[149],"clinical":[152],"hepatitis":[153],"C":[154],"infected":[159],"patient":[160],"discovered":[162],"novel":[164],"deletion":[165],"length":[167],"357\u00b1167":[168],"bp":[169],"that":[170],"was":[171],"validated":[172],"by":[173],"two":[174],"independent":[175],"long-read":[176],"experiments.":[178],"available":[181],"https://github.com/armintoepfer/haploclique.":[183],"A":[184],"summary":[185],"this":[187],"paper":[188],"appears":[189],"in":[190],"proceedings":[192],"RECOMB":[195],"2014":[196],"conference,":[197],"April":[198],"2-5.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":13},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":6}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}