{"id":"https://openalex.org/W3116401639","doi":"https://doi.org/10.1186/s12859-020-03811-z","title":"Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences","display_name":"Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3116401639","doi":"https://doi.org/10.1186/s12859-020-03811-z","mag":"3116401639","pmid":"https://pubmed.ncbi.nlm.nih.gov/33375937"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03811-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03811-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03811-z","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/s12859-020-03811-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018798814","display_name":"David S. Campo","orcid":"https://orcid.org/0000-0002-8970-3436"},"institutions":[{"id":"https://openalex.org/I1289490764","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12","country_code":"US","type":"funder","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David S. Campo","raw_affiliation_strings":["Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA. fyv6@cdc.gov","Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA. fyv6@cdc.gov","institution_ids":[]},{"raw_affiliation_string":"Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA","institution_ids":["https://openalex.org/I1289490764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085435304","display_name":"Yury Khudyakov","orcid":null},"institutions":[{"id":"https://openalex.org/I1289490764","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12","country_code":"US","type":"funder","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yury Khudyakov","raw_affiliation_strings":["Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA","institution_ids":["https://openalex.org/I1289490764"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5018798814"],"corresponding_institution_ids":["https://openalex.org/I1289490764"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21385675,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"S18","first_page":"482","last_page":"482"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9793999791145325,"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":0.9771999716758728,"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/hamming-space","display_name":"Hamming space","score":0.6255893707275391},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5675265789031982},{"id":"https://openalex.org/keywords/convex-hull","display_name":"Convex hull","score":0.5646023750305176},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.5442890524864197},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.521390974521637},{"id":"https://openalex.org/keywords/hamming-distance","display_name":"Hamming distance","score":0.49718502163887024},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4888876974582672},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.43892234563827515},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4216371774673462},{"id":"https://openalex.org/keywords/hamming-code","display_name":"Hamming code","score":0.33018916845321655},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32720309495925903},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3019466698169708},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2545865774154663},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2480274736881256},{"id":"https://openalex.org/keywords/regular-polygon","display_name":"Regular polygon","score":0.1894134283065796}],"concepts":[{"id":"https://openalex.org/C2779494224","wikidata":"https://www.wikidata.org/wiki/Q5645799","display_name":"Hamming space","level":5,"score":0.6255893707275391},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5675265789031982},{"id":"https://openalex.org/C206194317","wikidata":"https://www.wikidata.org/wiki/Q1138624","display_name":"Convex hull","level":3,"score":0.5646023750305176},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5442890524864197},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.521390974521637},{"id":"https://openalex.org/C193319292","wikidata":"https://www.wikidata.org/wiki/Q272172","display_name":"Hamming distance","level":2,"score":0.49718502163887024},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4888876974582672},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.43892234563827515},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4216371774673462},{"id":"https://openalex.org/C73150493","wikidata":"https://www.wikidata.org/wiki/Q853922","display_name":"Hamming code","level":4,"score":0.33018916845321655},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32720309495925903},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3019466698169708},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2545865774154663},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2480274736881256},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.1894134283065796},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C157125643","wikidata":"https://www.wikidata.org/wiki/Q884707","display_name":"Block code","level":3,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-03811-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03811-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03811-z","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:33375937","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33375937","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:doaj.org/article:2ec858088fa54aec85528f6ed1a154d6","is_oa":true,"landing_page_url":"https://doaj.org/article/2ec858088fa54aec85528f6ed1a154d6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 21, Iss S18, Pp 1-13 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7772912","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7772912","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03811-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03811-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03811-z","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":[{"score":0.8700000047683716,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3116401639.pdf","grobid_xml":"https://content.openalex.org/works/W3116401639.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1502916507","https://openalex.org/W1585110030","https://openalex.org/W2014472957","https://openalex.org/W2029301444","https://openalex.org/W2030525503","https://openalex.org/W2033781392","https://openalex.org/W2055043387","https://openalex.org/W2057000344","https://openalex.org/W2071949631","https://openalex.org/W2075013491","https://openalex.org/W2100191877","https://openalex.org/W2100548092","https://openalex.org/W2100936096","https://openalex.org/W2105145583","https://openalex.org/W2119057313","https://openalex.org/W2132492420","https://openalex.org/W2143677395","https://openalex.org/W2149230623","https://openalex.org/W2149906774","https://openalex.org/W2152565070","https://openalex.org/W2152850637","https://openalex.org/W2160265768","https://openalex.org/W2161087145","https://openalex.org/W2181468237","https://openalex.org/W2288266106","https://openalex.org/W2529384243","https://openalex.org/W2618599520","https://openalex.org/W2714497087","https://openalex.org/W2772837219","https://openalex.org/W2804358107","https://openalex.org/W2900195724","https://openalex.org/W2948936206","https://openalex.org/W4246947810","https://openalex.org/W4251391716"],"related_works":["https://openalex.org/W2371167013","https://openalex.org/W2182731056","https://openalex.org/W2613408642","https://openalex.org/W1519122282","https://openalex.org/W4235868261","https://openalex.org/W2098460688","https://openalex.org/W2140899540","https://openalex.org/W2169207476","https://openalex.org/W4380994333","https://openalex.org/W2158117886"],"abstract_inverted_index":{"CHD":[0],"is":[1],"a":[2],"fast":[3],"and":[4,22],"efficient":[5],"filtering":[6],"strategy":[7],"for":[8,46],"massively":[9],"reducing":[10],"the":[11,25,38],"computational":[12],"burden":[13],"of":[14,20,27],"pairwise":[15],"comparison":[16],"among":[17,30],"large":[18],"samples":[19],"sequences,":[21],"thus,":[23],"aiding":[24],"calculation":[26],"transmission":[28],"links":[29],"infected":[31],"individuals":[32],"using":[33],"threshold-based":[34],"methods.":[35],"In":[36],"addition,":[37],"convex":[39],"hull":[40],"efficiently":[41],"obtains":[42],"important":[43],"summary":[44],"metrics":[45],"intra-host":[47],"viral":[48],"populations.":[49]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
