{"id":"https://openalex.org/W2137604316","doi":"https://doi.org/10.1186/s13015-014-0030-4","title":"A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads","display_name":"A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads","publication_year":2015,"publication_date":"2015-01-15","ids":{"openalex":"https://openalex.org/W2137604316","doi":"https://doi.org/10.1186/s13015-014-0030-4","mag":"2137604316","pmid":"https://pubmed.ncbi.nlm.nih.gov/25648210"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-014-0030-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0030-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0030-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0030-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002115522","display_name":"Le Van Vinh","orcid":"https://orcid.org/0000-0001-5218-3089"},"institutions":[{"id":"https://openalex.org/I47265099","display_name":"Ho Chi Minh City University of Technology","ror":"https://ror.org/04qva2324","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I47265099"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Le Van Vinh","raw_affiliation_strings":["Faculty of Computer Science and Engineering, HCMC University of Technology, 268 Ly Thuong Kiet, Q10, Ho Chi Minh City, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Engineering, HCMC University of Technology, 268 Ly Thuong Kiet, Q10, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I47265099"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tran Van Lang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134642","display_name":"Lac Hong University","ror":"https://ror.org/03nypmk85","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210134642"]},{"id":"https://openalex.org/I70349855","display_name":"Vietnam Academy of Science and Technology","ror":"https://ror.org/02wsd5p50","country_code":"VN","type":"government","lineage":["https://openalex.org/I70349855"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Tran Van Lang","raw_affiliation_strings":["Institute of Applied Mechanics and Informatics, Vietnam Academy of Science and Technology (VAST), 01 Mac Dinh Chi, Q1, Ho Chi Minh City, Vietnam ; Faculty of Information Technology, Lac Hong University, 10 Huynh Van Nghe, Bien Hoa, Dong Nai Vietnam","Institute of Applied Mechanics and Informatics, Vietnam Academy of Science and Technology (VAST), 01 Mac Dinh Chi, Q1, Ho Chi Minh City, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Mechanics and Informatics, Vietnam Academy of Science and Technology (VAST), 01 Mac Dinh Chi, Q1, Ho Chi Minh City, Vietnam ; Faculty of Information Technology, Lac Hong University, 10 Huynh Van Nghe, Bien Hoa, Dong Nai Vietnam","institution_ids":["https://openalex.org/I70349855","https://openalex.org/I4210134642"]},{"raw_affiliation_string":"Institute of Applied Mechanics and Informatics, Vietnam Academy of Science and Technology (VAST), 01 Mac Dinh Chi, Q1, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I70349855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025738746","display_name":"L\u00ea Thanh B\u00ecnh","orcid":"https://orcid.org/0009-0009-3662-4396"},"institutions":[{"id":"https://openalex.org/I70349855","display_name":"Vietnam Academy of Science and Technology","ror":"https://ror.org/02wsd5p50","country_code":"VN","type":"government","lineage":["https://openalex.org/I70349855"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Le Thanh Binh","raw_affiliation_strings":["Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi Vietnam","Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi Vietnam","institution_ids":["https://openalex.org/I70349855"]},{"raw_affiliation_string":"Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam","institution_ids":["https://openalex.org/I70349855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073243218","display_name":"Tr\u1ea7n V\u0103n Ho\u00e0i","orcid":"https://orcid.org/0000-0002-0602-4287"},"institutions":[{"id":"https://openalex.org/I47265099","display_name":"Ho Chi Minh City University of Technology","ror":"https://ror.org/04qva2324","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I47265099"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Tran Van Hoai","raw_affiliation_strings":["Faculty of Computer Science and Engineering, HCMC University of Technology, 268 Ly Thuong Kiet, Q10, Ho Chi Minh City, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Engineering, HCMC University of Technology, 268 Ly Thuong Kiet, Q10, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I47265099"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210134642","https://openalex.org/I70349855"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":2.1082,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.8734471,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.44190001487731934,"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":0.44190001487731934,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.24250000715255737,"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/T10885","display_name":"Gene expression and cancer classification","score":0.048500001430511475,"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/metagenomics","display_name":"Metagenomics","score":0.847281813621521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7405551075935364},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5973250865936279},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.596805214881897},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44018465280532837},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3288663625717163},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10162606835365295}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.847281813621521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7405551075935364},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5973250865936279},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.596805214881897},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44018465280532837},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3288663625717163},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10162606835365295},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13015-014-0030-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0030-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0030-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:25648210","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25648210","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:europepmc.org:3282290","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4304631","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/s13015-014-0030-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-014-0030-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-014-0030-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137604316.pdf","grobid_xml":"https://content.openalex.org/works/W2137604316.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W46815989","https://openalex.org/W1539550196","https://openalex.org/W1565050238","https://openalex.org/W1875047762","https://openalex.org/W1997673861","https://openalex.org/W2006465310","https://openalex.org/W2020069326","https://openalex.org/W2021380741","https://openalex.org/W2029437806","https://openalex.org/W2048818637","https://openalex.org/W2061680337","https://openalex.org/W2082203850","https://openalex.org/W2097160089","https://openalex.org/W2106651224","https://openalex.org/W2112888758","https://openalex.org/W2113601822","https://openalex.org/W2116895571","https://openalex.org/W2120048439","https://openalex.org/W2122646534","https://openalex.org/W2124637227","https://openalex.org/W2125826054","https://openalex.org/W2131988453","https://openalex.org/W2135780060","https://openalex.org/W2139436782","https://openalex.org/W2140604849","https://openalex.org/W2144467924","https://openalex.org/W2150208009","https://openalex.org/W2150593711","https://openalex.org/W2155563453","https://openalex.org/W2156995746","https://openalex.org/W2157107905","https://openalex.org/W2162039942","https://openalex.org/W2162210683","https://openalex.org/W2164327068","https://openalex.org/W2405577833","https://openalex.org/W2477408078","https://openalex.org/W2482651110","https://openalex.org/W2487925669","https://openalex.org/W2914081640","https://openalex.org/W4213283310"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W4388282505","https://openalex.org/W3198631238","https://openalex.org/W4255657129"],"abstract_inverted_index":{"BACKGROUND:":[0],"Metagenomics":[1],"is":[2,30,77,93],"the":[3,20,44,51,65,99,102,131,135,147,153,218],"study":[4],"of":[5,15,19,64,67,101,115,127,134,163,165,205],"genetic":[6],"materials":[7],"derived":[8],"directly":[9],"from":[10,16,39,56,117],"complex":[11],"microbial":[12],"samples,":[13],"instead":[14],"culture.":[17],"One":[18],"crucial":[21],"steps":[22],"in":[23,62,90,120,225],"metagenomic":[24,122,206],"analysis,":[25],"referred":[26],"to":[27,31,97],"as":[28],"\"binning\",":[29],"separate":[32],"reads":[33,116,137,189],"into":[34,140],"clusters":[35],"that":[36,177],"represent":[37],"genomes":[38],"closely":[40],"related":[41],"organisms.":[42],"Among":[43],"existing":[45],"binning":[46,114,182,204],"methods,":[47],"unsupervised":[48,109],"methods":[49],"base":[50],"classification":[52],"on":[53,143,159,171],"features":[54],"extracted":[55],"reads,":[57,207],"and":[58,84,173,187,200,220],"especially":[59],"taking":[60],"advantage":[61],"case":[63],"limitation":[66],"reference":[68,213],"database":[69],"availability.":[70],"However,":[71],"their":[72],"performance,":[73],"under":[74],"various":[75],"aspects,":[76],"still":[78],"being":[79],"investigated":[80],"by":[81,155],"recent":[82],"theoretical":[83],"empirical":[85],"studies.":[86],"The":[87,124,149,168,215],"one":[88],"addressed":[89],"this":[91,226],"paper":[92,106,196,227],"among":[94],"those":[95],"efforts":[96],"enhance":[98],"accuracy":[100],"classification.":[103],"RESULTS:":[104],"This":[105,195],"presents":[107],"an":[108,157],"algorithm,":[110,136],"called":[111],"BiMeta,":[112],"for":[113,184,203],"different":[118],"species":[119],"a":[121,198],"dataset.":[123],"algorithm":[125,202,219],"consists":[126],"two":[128],"phases.":[129],"In":[130],"first":[132],"phase":[133,151],"are":[138],"grouped":[139],"groups":[141,154],"based":[142],"overlap":[144],"information":[145],"between":[146],"reads.":[148,167],"second":[150],"merges":[152],"using":[156],"observation":[158],"l-mer":[160],"frequency":[161],"distribution":[162],"sets":[164],"non-overlapping":[166],"experimental":[169],"results":[170],"simulated":[172],"real":[174],"datasets":[175,223],"showed":[176],"BiMeta":[178],"outperforms":[179],"three":[180],"state-of-the-art":[181],"algorithms":[183],"both":[185],"short":[186],"long":[188],"(\u2265700":[190],"b":[191],"p)":[192],"datasets.":[193],"CONCLUSIONS:":[194],"developed":[197],"novel":[199],"efficient":[201],"which":[208],"does":[209],"not":[210],"require":[211],"any":[212],"database.":[214],"software":[216],"implementing":[217],"all":[221],"test":[222],"mentioned":[224],"can":[228],"be":[229],"downloaded":[230],"at":[231],"http://it.hcmute.edu.vn/bioinfo/bimeta/index.htm.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}