{"id":"https://openalex.org/W2986181758","doi":"https://doi.org/10.1186/s12859-019-3138-1","title":"A binning tool to reconstruct viral haplotypes from assembled contigs","display_name":"A binning tool to reconstruct viral haplotypes from assembled contigs","publication_year":2019,"publication_date":"2019-11-04","ids":{"openalex":"https://openalex.org/W2986181758","doi":"https://doi.org/10.1186/s12859-019-3138-1","mag":"2986181758","pmid":"https://pubmed.ncbi.nlm.nih.gov/31684876"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3138-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3138-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3138-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3138-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100441162","display_name":"Jiao Chen","orcid":"https://orcid.org/0000-0001-5737-0561"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiao Chen","raw_affiliation_strings":["Computer Science and Engineering, Michigan State University, East Lansing, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Michigan State University, East Lansing, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083607843","display_name":"Jiayu Shang","orcid":"https://orcid.org/0000-0001-5974-4985"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiayu Shang","raw_affiliation_strings":["Electrical Engineering, City University of Hong Kong, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical Engineering, City University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102003659","display_name":"Jianrong Wang","orcid":"https://orcid.org/0000-0002-9290-4888"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianrong Wang","raw_affiliation_strings":["Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081855118","display_name":"Yanni Sun","orcid":"https://orcid.org/0000-0003-1373-8023"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Yanni Sun","raw_affiliation_strings":["Electrical Engineering, City University of Hong Kong, Hong Kong, China. yannisun@cityu.edu.hk","Electrical Engineering, City University of Hong Kong, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0003-1373-8023","affiliations":[{"raw_affiliation_string":"Electrical Engineering, City University of Hong Kong, Hong Kong, China. yannisun@cityu.edu.hk","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Electrical Engineering, City University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5081855118"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.0759,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43736255,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"1","first_page":"544","last_page":"544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7975999712944031,"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":0.7975999712944031,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.03579999879002571,"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/T10112","display_name":"HIV Research and Treatment","score":0.03200000151991844,"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/contig","display_name":"Contig","score":0.9351384043693542},{"id":"https://openalex.org/keywords/viral-quasispecies","display_name":"Viral quasispecies","score":0.7910104990005493},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.7431707382202148},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5909442901611328},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5892794728279114},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5492947697639465},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5430819392204285},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45432204008102417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1896037459373474},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.12429073452949524}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9351384043693542},{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.7910104990005493},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7431707382202148},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5909442901611328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5892794728279114},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5492947697639465},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5430819392204285},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45432204008102417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1896037459373474},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.12429073452949524}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D012327","descriptor_name":"RNA Virus Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D012327","descriptor_name":"RNA Virus Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D012327","descriptor_name":"RNA Virus Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D012327","descriptor_name":"RNA Virus Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","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":"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":"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":5,"locations":[{"id":"doi:10.1186/s12859-019-3138-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3138-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3138-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31684876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31684876","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/dcd006a4-55b6-4ed3-9a54-12babea5931d","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/dcd006a4-55b6-4ed3-9a54-12babea5931d","pdf_url":"https://scholars.cityu.edu.hk/files/78216867/s12859_019_3138_1.pdf","source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Chen, J, Shang, J, Wang, J & Sun, Y 2019, 'A binning tool to reconstruct viral haplotypes from assembled contigs', BMC Bioinformatics, vol. 20, 544. https://doi.org/10.1186/s12859-019-3138-1","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:21412c0be12e4657b2bc656d2d4dd86f","is_oa":true,"landing_page_url":"https://doaj.org/article/21412c0be12e4657b2bc656d2d4dd86f","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":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5803292","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6829986","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3138-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3138-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3138-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6399999856948853,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1028460376","display_name":null,"funder_award_id":"7200620","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320310016","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993"},{"id":"https://openalex.org/F4320332431","display_name":"College of Engineering, Michigan State University","ror":"https://ror.org/05hs6h993"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2986181758.pdf","grobid_xml":"https://content.openalex.org/works/W2986181758.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W604170243","https://openalex.org/W1433995531","https://openalex.org/W1565377632","https://openalex.org/W1584790813","https://openalex.org/W1703384511","https://openalex.org/W1983511569","https://openalex.org/W2025161234","https://openalex.org/W2027969303","https://openalex.org/W2042704442","https://openalex.org/W2057421874","https://openalex.org/W2069572775","https://openalex.org/W2079958213","https://openalex.org/W2103901746","https://openalex.org/W2105252537","https://openalex.org/W2105757606","https://openalex.org/W2110233077","https://openalex.org/W2115501618","https://openalex.org/W2121291798","https://openalex.org/W2131271579","https://openalex.org/W2140366683","https://openalex.org/W2141920662","https://openalex.org/W2142678478","https://openalex.org/W2157539385","https://openalex.org/W2167469524","https://openalex.org/W2175526948","https://openalex.org/W2336086067","https://openalex.org/W2341364667","https://openalex.org/W2586360538","https://openalex.org/W2607297980","https://openalex.org/W2760526698","https://openalex.org/W2789208418","https://openalex.org/W2808035849","https://openalex.org/W2949491511","https://openalex.org/W2950774292","https://openalex.org/W3014294420","https://openalex.org/W4230982365","https://openalex.org/W4242285942","https://openalex.org/W4392543504"],"related_works":["https://openalex.org/W2370565492","https://openalex.org/W2016766059","https://openalex.org/W2029741357","https://openalex.org/W1992950355","https://openalex.org/W4381279187","https://openalex.org/W2115108201","https://openalex.org/W2013063066","https://openalex.org/W2108742089","https://openalex.org/W2412948090","https://openalex.org/W2472738690"],"abstract_inverted_index":{"BACKGROUND:":[0],"Infections":[1],"by":[2],"RNA":[3,173],"viruses":[4],"such":[5],"as":[6],"Influenza,":[7],"HIV":[8],"still":[9,84,124],"pose":[10],"a":[11,85,101,112,129,145,191,247],"serious":[12],"threat":[13],"to":[14,52,179,186,190],"human":[15],"health":[16],"despite":[17],"extensive":[18],"research":[19],"on":[20,151,197,212,269],"viral":[21,76,160,237,257,270],"diseases.":[22],"One":[23],"challenge":[24],"for":[25,74,172,236,252],"producing":[26],"effective":[27],"prevention":[28],"and":[29,54,66,69,154,168,207,210,229],"treatment":[30],"strategies":[31],"is":[32,49,83,123],"high":[33,165,260],"intra-species":[34],"genetic":[35,47],"diversity.":[36],"As":[37,100],"different":[38,42,138,203,256],"strains":[39,68],"may":[40],"have":[41],"biological":[43],"properties,":[44],"characterizing":[45],"the":[46,108,226],"diversity":[48],"thus":[50],"important":[51],"vaccine":[53],"drug":[55],"design.":[56],"Next-generation":[57],"sequencing":[58,75,170,200,215],"technology":[59],"enables":[60],"comprehensive":[61],"characterization":[62],"of":[63,81,111,163,231],"both":[64],"known":[65],"novel":[67],"has":[70],"been":[71],"widely":[72],"adopted":[73],"populations.":[77],"However,":[78],"genome-scale":[79,121],"reconstruction":[80],"haplotypes":[82,122,161,258],"challenging":[86],"problem.":[87],"In":[88,241],"particular,":[89],"haplotype":[90,204,238],"assembly":[91],"programs":[92],"often":[93],"produce":[94],"contigs":[95,119,136,254],"rather":[96],"than":[97],"full":[98],"genomes.":[99],"mutation":[102,113],"in":[103,233],"one":[104],"gene":[105],"can":[106],"mask":[107],"phenotypic":[109],"effects":[110],"at":[114],"another":[115],"locus,":[116],"clustering":[117,178],"these":[118],"into":[120,137],"needed.":[125],"RESULTS:":[126],"We":[127],"developed":[128],"contig":[130,155,208,222,234,249,271],"binning":[131,223,235,250],"tool,":[132],"VirBin,":[133,246],"which":[134],"clusters":[135],"groups":[139],"so":[140],"that":[141,182],"each":[142],"group":[143],"represents":[144],"haplotype.":[146,192],"Commonly":[147],"used":[148],"features":[149],"based":[150],"sequence":[152,166,261],"composition":[153],"coverage":[156,171],"cannot":[157],"effectively":[158],"distinguish":[159],"because":[162],"their":[164],"similarity":[167],"heterogeneous":[169],"viruses.":[174],"VirBin":[175,232],"applied":[176],"prototype-based":[177],"cluster":[180],"regions":[181],"are":[183,276],"more":[184],"likely":[185],"contain":[187],"mutations":[188],"specific":[189],"The":[193,217,273],"tool":[194,251],"was":[195],"tested":[196],"multiple":[198],"simulated":[199],"data":[201],"with":[202,220,259,266],"abundance":[205],"distributions":[206],"sizes,":[209],"also":[211],"mock":[213],"quasispecies":[214],"data.":[216],"benchmark":[218],"results":[219],"other":[221,267],"tools":[224,268],"demonstrated":[225],"superior":[227],"sensitivity":[228],"precision":[230],"reconstruction.":[239],"CONCLUSIONS:":[240],"this":[242],"work,":[243],"we":[244],"presented":[245],"new":[248],"distinguishing":[253],"from":[255],"similarity.":[262],"It":[263],"competes":[264],"favorably":[265],"binning.":[272],"source":[274],"codes":[275],"available":[277],"at:":[278],"https://github.com/chjiao/VirBin":[279],".":[280]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}