{"id":"https://openalex.org/W2189527770","doi":"https://doi.org/10.1109/iccabs.2015.7344730","title":"2SNV: Quasispecies reconstruction from PacBio reads","display_name":"2SNV: Quasispecies reconstruction from PacBio reads","publication_year":2015,"publication_date":"2015-10-01","ids":{"openalex":"https://openalex.org/W2189527770","doi":"https://doi.org/10.1109/iccabs.2015.7344730","mag":"2189527770"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2015.7344730","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2015.7344730","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074859035","display_name":"Alexander Artyomenko","orcid":"https://orcid.org/0000-0002-5635-3118"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander Artyomenko","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037737527","display_name":"Nicholas C. Wu","orcid":"https://orcid.org/0000-0002-9078-6697"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas C. Wu","raw_affiliation_strings":["Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, CA"],"affiliations":[{"raw_affiliation_string":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, CA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017101305","display_name":"Serghei Mangul","orcid":"https://orcid.org/0000-0003-4770-3443"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Serghei Mangul","raw_affiliation_strings":["Computer Science Department"],"affiliations":[{"raw_affiliation_string":"Computer Science Department","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009368988","display_name":"Eleazar Eskin","orcid":"https://orcid.org/0000-0003-1149-4758"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eleazar Eskin","raw_affiliation_strings":["Computer Science Department"],"affiliations":[{"raw_affiliation_string":"Computer Science Department","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029398617","display_name":"Ren Sun","orcid":"https://orcid.org/0000-0002-8628-7019"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ren Sun","raw_affiliation_strings":["Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA"],"affiliations":[{"raw_affiliation_string":"Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072751459","display_name":"Alex Zelikovsky","orcid":"https://orcid.org/0000-0003-4424-4691"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Zelikovsky","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA","institution_ids":["https://openalex.org/I181565077"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5074859035"],"corresponding_institution_ids":["https://openalex.org/I181565077"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06627474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9923999905586243,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9905999898910522,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/viral-quasispecies","display_name":"Viral quasispecies","score":0.8631801605224609},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5651358366012573},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.5099366903305054},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.45378634333610535},{"id":"https://openalex.org/keywords/cover","display_name":"Cover (algebra)","score":0.4498637020587921},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42321568727493286},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4212430417537689},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39831387996673584},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28350895643234253},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.16447186470031738},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.16368836164474487},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1485641598701477},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1435984969139099},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07003283500671387}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.8631801605224609},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5651358366012573},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.5099366903305054},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.45378634333610535},{"id":"https://openalex.org/C2780428219","wikidata":"https://www.wikidata.org/wiki/Q16952335","display_name":"Cover (algebra)","level":2,"score":0.4498637020587921},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42321568727493286},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4212430417537689},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39831387996673584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28350895643234253},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16447186470031738},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.16368836164474487},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1485641598701477},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1435984969139099},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07003283500671387},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2015.7344730","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2015.7344730","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life below water","score":0.9100000262260437,"id":"https://metadata.un.org/sdg/14"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W1981558659","https://openalex.org/W2002556659","https://openalex.org/W2103441770","https://openalex.org/W2163326395"],"related_works":["https://openalex.org/W2370565492","https://openalex.org/W2016766059","https://openalex.org/W2029741357","https://openalex.org/W2144907742","https://openalex.org/W1748700469","https://openalex.org/W2009366069","https://openalex.org/W2620872782","https://openalex.org/W2086431635","https://openalex.org/W2073918065","https://openalex.org/W2417258543"],"abstract_inverted_index":{"Pacific":[0],"Biosciences":[1],"(PacBio)":[2],"sequencing":[3],"is":[4,21],"providing":[5],"thousands":[6],"of":[7,27],"reads":[8,67],"with":[9,75],"the":[10,84],"length":[11,20],"up":[12],"to":[13,23,65,82],"10,000":[14],"bases.":[15],"In":[16],"most":[17,86],"cases":[18],"this":[19,30],"enough":[22],"cover":[24],"entire":[25],"region":[26],"interest":[28],"however":[29],"technology":[31],"has":[32],"high":[33],"(\u224815%)":[34],"error":[35],"rate.":[36],"We":[37],"propose":[38],"a":[39],"method":[40,51,79],"for":[41,60],"viral":[42],"haplotype":[43],"reconstruction":[44],"using":[45],"long":[46],"SMRT":[47],"reads.":[48],"The":[49],"proposed":[50],"based":[52],"on":[53],"correlation":[54],"between":[55],"SNVs":[56],"and":[57],"maximum":[58],"likelihood":[59],"frequency":[61],"estimation.":[62],"When":[63],"applied":[64],"PacBio":[66],"from":[68],"an":[69],"Influenza":[70],"A":[71],"Virus":[72],"(IAV)":[73],"sample":[74],"ten":[76],"variants,":[77],"our":[78],"was":[80],"able":[81],"reconstruct":[83],"nine":[85],"frequent.":[87]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}