{"id":"https://openalex.org/W2771514818","doi":"https://doi.org/10.1093/bioinformatics/btx810","title":"fMLC: fast multi-level clustering and visualization of large molecular datasets","display_name":"fMLC: fast multi-level clustering and visualization of large molecular datasets","publication_year":2017,"publication_date":"2017-12-14","ids":{"openalex":"https://openalex.org/W2771514818","doi":"https://doi.org/10.1093/bioinformatics/btx810","mag":"2771514818","pmid":"https://pubmed.ncbi.nlm.nih.gov/29253070"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1577/25120779/btx810.pdf","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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1577/25120779/btx810.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047169486","display_name":"Duong Vu","orcid":"https://orcid.org/0000-0001-7960-2765"},"institutions":[{"id":"https://openalex.org/I4210113371","display_name":"Westerdijk Fungal Biodiversity Institute","ror":"https://ror.org/030a5r161","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1322597698","https://openalex.org/I4210113371"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"D Vu","raw_affiliation_strings":["Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210113371"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060758353","display_name":"Sonja Georgievska","orcid":"https://orcid.org/0000-0002-8094-4532"},"institutions":[{"id":"https://openalex.org/I4210095242","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800991832","https://openalex.org/I4210090210","https://openalex.org/I4210095242"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"S Georgievska","raw_affiliation_strings":["Netherlands eScience Center, XG Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands eScience Center, XG Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210095242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031175598","display_name":"Sz\u00e1niszl\u00f3 Sz\u00f6ke","orcid":null},"institutions":[{"id":"https://openalex.org/I4210113371","display_name":"Westerdijk Fungal Biodiversity Institute","ror":"https://ror.org/030a5r161","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1322597698","https://openalex.org/I4210113371"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"S Szoke","raw_affiliation_strings":["Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210113371"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077797266","display_name":"Arnold Kuzniar","orcid":"https://orcid.org/0000-0003-1711-7961"},"institutions":[{"id":"https://openalex.org/I4210095242","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800991832","https://openalex.org/I4210090210","https://openalex.org/I4210095242"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"A Kuzniar","raw_affiliation_strings":["Netherlands eScience Center, XG Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Netherlands eScience Center, XG Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210095242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101955637","display_name":"Vincent Robert","orcid":"https://orcid.org/0000-0002-9370-4677"},"institutions":[{"id":"https://openalex.org/I4210113371","display_name":"Westerdijk Fungal Biodiversity Institute","ror":"https://ror.org/030a5r161","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1322597698","https://openalex.org/I4210113371"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"V Robert","raw_affiliation_strings":["Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics group, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210113371"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5047169486","https://openalex.org/A5101955637"],"corresponding_institution_ids":["https://openalex.org/I4210113371"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4485,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.64626566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"34","issue":"9","first_page":"1577","last_page":"1579"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6805999875068665,"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":0.6805999875068665,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.07760000228881836,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.05469999834895134,"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/visualization","display_name":"Visualization","score":0.8439270257949829},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.8128690719604492},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7573273777961731},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.5783314108848572},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5586345791816711},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.541957437992096},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47345632314682007},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.4471023976802826},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.18307390809059143},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12920406460762024}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.8439270257949829},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8128690719604492},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7573273777961731},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.5783314108848572},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5586345791816711},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.541957437992096},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47345632314682007},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.4471023976802826},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18307390809059143},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12920406460762024},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1577/25120779/btx810.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29253070","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29253070","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:knaw:oai:pure.knaw.nl:publications/0ab697b5-1db1-4342-a30c-3dbb222f7ab3","is_oa":false,"landing_page_url":"https://pure.knaw.nl/portal/en/publications/0ab697b5-1db1-4342-a30c-3dbb222f7ab3","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1577/25120779/btx810.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320314239","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2771514818.pdf","grobid_xml":"https://content.openalex.org/works/W2771514818.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1489838709","https://openalex.org/W1875842236","https://openalex.org/W2046821185","https://openalex.org/W2058720919","https://openalex.org/W2110734043","https://openalex.org/W2124351063","https://openalex.org/W2158714788","https://openalex.org/W2163762600","https://openalex.org/W2170747616","https://openalex.org/W2176645417","https://openalex.org/W2549075672","https://openalex.org/W2950954328"],"related_works":["https://openalex.org/W2100807713","https://openalex.org/W2077600704","https://openalex.org/W2359998128","https://openalex.org/W2585466406","https://openalex.org/W2557714193","https://openalex.org/W2150394469","https://openalex.org/W2888523397","https://openalex.org/W2380798983","https://openalex.org/W3181788097","https://openalex.org/W2098924604"],"abstract_inverted_index":{"Motivation:":[0],"Despite":[1],"successful":[2],"applications":[3],"of":[4],"data":[5],"clustering":[6],"and":[7,56,74,89],"visualization":[8,48],"techniques":[9],"in":[10],"molecular":[11],"sequence":[12],"identification,":[13],"current":[14],"technologies":[15],"still":[16],"do":[17],"not":[18],"scale":[19],"to":[20,37,53,72],"large":[21],"biological":[22],"datasets.":[23],"Results:":[24],"We":[25],"address":[26],"this":[27],"problem":[28],"by":[29],"a":[30],"new":[31],"multi-threaded":[32],"tool,":[33],"fMLC,":[34],"primarily":[35],"developed":[36],"cluster":[38,55,75],"DNA":[39],"sequences,":[40],"that":[41],"is":[42,79],"supplemented":[43],"with":[44],"an":[45],"interactive":[46],"web-based":[47],"component,":[49],"DiVE.":[50],"fMLC":[51],"enabled":[52],"compare,":[54],"visualize":[57],"350K":[58],"ITS":[59],"fungal":[60],"sequences":[61],"at":[62],"the":[63,76,84],"species":[64],"level.":[65],"It":[66],"took":[67],"less":[68],"than":[69,83],"two":[70],"hours":[71],"compare":[73],"dataset,":[77],"which":[78],"twelve":[80],"times":[81],"faster":[82],"time":[85],"reported":[86],"previously.":[87],"Availability":[88],"implementation:":[90],"https://github.com/FastMLC/fMLC":[91],"(doi:":[92],"10.5281/zenodo.926820).":[93],"Contact:":[94],"d.vu@westerdijkinstitute.nl":[95],"or":[96],"v.robert@westerdijkinstitute.nl.":[97]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
