{"id":"https://openalex.org/W2952396481","doi":"https://doi.org/10.1109/bibm.2018.8621235","title":"deSPI: efficient classification of metagenomics reads with lightweight de Bruijn graph-based reference indexing","display_name":"deSPI: efficient classification of metagenomics reads with lightweight de Bruijn graph-based reference indexing","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2952396481","doi":"https://doi.org/10.1109/bibm.2018.8621235","mag":"2952396481"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621235","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621235","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5077353618","display_name":"Dengfeng Guan","orcid":"https://orcid.org/0000-0002-6376-3940"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dengfeng Guan","raw_affiliation_strings":["dept. of Computer Science, Harbin Institute of Technology, Harbin, China"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100461657","display_name":"Bo Liu","orcid":"https://orcid.org/0000-0002-4414-4001"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["dept. of Computer Science, Harbin Institute of Technology, Harbin, China"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392447","display_name":"Yadong Wang","orcid":"https://orcid.org/0000-0001-6500-6217"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yadong Wang","raw_affiliation_strings":["dept. of Computer Science, Harbin Institute of Technology, Harbin, China"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077353618"],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":null,"apc_paid":null,"fwci":0.2758,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.58052291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":null,"first_page":"265","last_page":"269"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9908000230789185,"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":0.9904999732971191,"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/de-bruijn-graph","display_name":"De Bruijn graph","score":0.9458572864532471},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7186024785041809},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.662502646446228},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6576094627380371},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.5728352665901184},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5628730654716492},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4249518811702728},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4141482710838318},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32993799448013306},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2314717173576355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14901688694953918},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09761592745780945}],"concepts":[{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.9458572864532471},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7186024785041809},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.662502646446228},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6576094627380371},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.5728352665901184},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5628730654716492},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4249518811702728},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4141482710838318},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32993799448013306},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2314717173576355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14901688694953918},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09761592745780945},{"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},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621235","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621235","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W2003347102","https://openalex.org/W2055043387","https://openalex.org/W2107903949","https://openalex.org/W2143777796","https://openalex.org/W2158322625","https://openalex.org/W2159954944","https://openalex.org/W2171571559","https://openalex.org/W2337747100","https://openalex.org/W2474973645","https://openalex.org/W2951160681","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2562683361","https://openalex.org/W3087469195","https://openalex.org/W2354744388","https://openalex.org/W3125399386","https://openalex.org/W2949121831","https://openalex.org/W2756186577","https://openalex.org/W2735897904","https://openalex.org/W3215786367","https://openalex.org/W2107854630","https://openalex.org/W1908987670"],"abstract_inverted_index":{"One":[0],"of":[1,10,54],"the":[2,8],"core":[3],"problems":[4],"in":[5,18],"metagenomics":[6],"is":[7],"classification":[9,22,43],"shotgun":[11],"sequencing":[12],"reads":[13,86],"to":[14,67],"identify":[15],"species":[16],"present":[17],"samples.":[19],"Many":[20],"supervised":[21],"tools":[23],"have":[24],"been":[25],"developed":[26],"recently,":[27],"but":[28],"they":[29],"either":[30],"consume":[31],"large":[32,35],"memory":[33,79],"or":[34],"computation":[36],"time.":[37],"Herein":[38],"we":[39],"propose":[40],"a":[41,63,95],"new":[42],"method,":[44],"de":[45,55],"Bruijn":[46,56],"Graph-based":[47],"Species":[48],"Identifier":[49],"(deSPI),":[50],"which":[51],"takes":[52],"advantage":[53],"graph":[57],"and":[58,62,82,84,91,98],"FM-index":[59],"data":[60],"structures":[61],"hierarchical":[64],"top-down":[65],"strategy":[66],"do":[68],"classification.":[69],"The":[70],"experimental":[71],"results":[72],"suggest":[73],"that":[74],"deSPI":[75],"uses":[76],"much":[77,87],"less":[78],"than":[80,89],"Clark":[81],"Kraken":[83],"classifies":[85],"faster":[88],"Centrifuge":[90],"Kaiju,":[92],"while":[93],"maintaining":[94],"comparable":[96],"sensitivity":[97],"accuracy.":[99]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
