{"id":"https://openalex.org/W3146880806","doi":"https://doi.org/10.1093/bioinformatics/btab234","title":"HierCC: a multi-level clustering scheme for population assignments based on core genome MLST","display_name":"HierCC: a multi-level clustering scheme for population assignments based on core genome MLST","publication_year":2021,"publication_date":"2021-04-06","ids":{"openalex":"https://openalex.org/W3146880806","doi":"https://doi.org/10.1093/bioinformatics/btab234","mag":"3146880806","pmid":"https://pubmed.ncbi.nlm.nih.gov/33823553"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab234","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btab234","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091225885","display_name":"Zhemin Zhou","orcid":"https://orcid.org/0000-0001-9783-0366"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["CN","GB"],"is_corresponding":true,"raw_author_name":"Zhemin Zhou","raw_affiliation_strings":["Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","Pasteurien College, Soochow University, Suzhou, China","Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Pasteurien College, Soochow University, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077961117","display_name":"Jane Charlesworth","orcid":"https://orcid.org/0000-0001-9759-9838"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Jane Charlesworth","raw_affiliation_strings":["Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","Pasteurien College, Soochow University, Suzhou, China","Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Pasteurien College, Soochow University, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045135220","display_name":"Mark Achtman","orcid":"https://orcid.org/0000-0001-6815-0070"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Mark Achtman","raw_affiliation_strings":["Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom","Pasteurien College, Soochow University, Suzhou, China"],"affiliations":[{"raw_affiliation_string":"Warwick Medical School, University of Warwick , Coventry CV4 7AL, UK","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Pasteurien College, Soochow University, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5091225885"],"corresponding_institution_ids":["https://openalex.org/I3923682","https://openalex.org/I39555362"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.4497,"has_fulltext":false,"cited_by_count":117,"citation_normalized_percentile":{"value":0.97079573,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"37","issue":"20","first_page":"3645","last_page":"3646"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9890999794006348,"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":0.9890999794006348,"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/T12232","display_name":"Yersinia bacterium, plague, ectoparasites research","score":0.9785000085830688,"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/T10066","display_name":"Gut microbiota and health","score":0.9623000025749207,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.6763205528259277},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6376107335090637},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.6109737753868103},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5036110281944275},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4842934012413025},{"id":"https://openalex.org/keywords/multilocus-sequence-typing","display_name":"Multilocus sequence typing","score":0.4827553629875183},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47249022126197815},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44302475452423096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2960135340690613},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2943676710128784},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24190416932106018},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12989374995231628},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10708460211753845},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.09867307543754578},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.06714999675750732}],"concepts":[{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.6763205528259277},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6376107335090637},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.6109737753868103},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5036110281944275},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4842934012413025},{"id":"https://openalex.org/C77434933","wikidata":"https://www.wikidata.org/wiki/Q4043440","display_name":"Multilocus sequence typing","level":4,"score":0.4827553629875183},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47249022126197815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44302475452423096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2960135340690613},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2943676710128784},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24190416932106018},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12989374995231628},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10708460211753845},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.09867307543754578},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.06714999675750732},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btab234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab234","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33823553","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33823553","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:wrap.warwick.ac.uk:151046","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400665","display_name":"Warwick Research Archive Portal (University of Warwick)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39555362","host_organization_name":"University of Warwick","host_organization_lineage":["https://openalex.org/I39555362"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:7434650","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8545296","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8545296","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8545296","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab234","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G651356483","display_name":null,"funder_award_id":"202792","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6695521049","display_name":null,"funder_award_id":"202792/Z/16/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1987971958","https://openalex.org/W2066084832","https://openalex.org/W2088535953","https://openalex.org/W2089216231","https://openalex.org/W2528608880","https://openalex.org/W2530546106","https://openalex.org/W2768017947","https://openalex.org/W2768707988","https://openalex.org/W2929327252","https://openalex.org/W2950050732","https://openalex.org/W2993005136","https://openalex.org/W3008965782","https://openalex.org/W3045684808","https://openalex.org/W6781663804"],"related_works":["https://openalex.org/W2941777425","https://openalex.org/W2030437188","https://openalex.org/W2145001255","https://openalex.org/W2132072542","https://openalex.org/W1898047497","https://openalex.org/W2569062348","https://openalex.org/W2396926696","https://openalex.org/W2275684745","https://openalex.org/W2154837539","https://openalex.org/W2953157660"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":40},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":6}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
