{"id":"https://openalex.org/W3126772331","doi":"https://doi.org/10.1109/bibm49941.2020.9313313","title":"MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics","display_name":"MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics","publication_year":2020,"publication_date":"2020-12-16","ids":{"openalex":"https://openalex.org/W3126772331","doi":"https://doi.org/10.1109/bibm49941.2020.9313313","mag":"3126772331"},"language":"en","primary_location":{"id":"doi:10.1109/bibm49941.2020.9313313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm49941.2020.9313313","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 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/A5047481354","display_name":"Wui Wang Lui","orcid":"https://orcid.org/0000-0002-6493-1651"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Wui Wang Lui","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042739197","display_name":"Amy Wing-Sze Leung","orcid":"https://orcid.org/0000-0002-1302-8032"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Amy W. S. Leung","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103578758","display_name":"Henry C. M. Leung","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Henry C. M. Leung","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100658562","display_name":"Xin Yan","orcid":"https://orcid.org/0000-0001-9253-3290"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yan Xin","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027057984","display_name":"Jade L. L. Teng","orcid":"https://orcid.org/0000-0002-3912-4057"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jade L. L. Teng","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017803324","display_name":"Patrick C. Y. Woo","orcid":"https://orcid.org/0000-0001-9401-1832"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Patrick C. Y. Woo","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077116003","display_name":"Tak\u2010Wah Lam","orcid":"https://orcid.org/0000-0003-4676-8587"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Tak-Wah Lam","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027440970","display_name":"Ruibang Luo","orcid":"https://orcid.org/0000-0001-9711-6533"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ruibang Luo","raw_affiliation_strings":["The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5047481354"],"corresponding_institution_ids":["https://openalex.org/I889458895"],"apc_list":null,"apc_paid":null,"fwci":0.0836,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.47094662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"329","last_page":"336"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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":0.9976000189781189,"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":0.8986035585403442},{"id":"https://openalex.org/keywords/minion","display_name":"Minion","score":0.8675519227981567},{"id":"https://openalex.org/keywords/refseq","display_name":"RefSeq","score":0.8045983910560608},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.6391406059265137},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6231815814971924},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.48223575949668884},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4742530882358551},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.452812135219574},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44030851125717163},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3831980526447296},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3807830214500427},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37532472610473633},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.293720543384552},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29362282156944275},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11649343371391296},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11599227786064148}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8986035585403442},{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.8675519227981567},{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.8045983910560608},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.6391406059265137},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6231815814971924},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.48223575949668884},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4742530882358551},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.452812135219574},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44030851125717163},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3831980526447296},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3807830214500427},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37532472610473633},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.293720543384552},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29362282156944275},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11649343371391296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11599227786064148},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm49941.2020.9313313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm49941.2020.9313313","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1967962707","https://openalex.org/W2019849264","https://openalex.org/W2103441770","https://openalex.org/W2109684694","https://openalex.org/W2119451273","https://openalex.org/W2134163835","https://openalex.org/W2134852597","https://openalex.org/W2143485490","https://openalex.org/W2150131459","https://openalex.org/W2264290069","https://openalex.org/W2468194934","https://openalex.org/W2561512876","https://openalex.org/W2592783371","https://openalex.org/W2607669908","https://openalex.org/W2765268335","https://openalex.org/W2765923508","https://openalex.org/W2789843538","https://openalex.org/W2790977261","https://openalex.org/W2897603717","https://openalex.org/W2921872415","https://openalex.org/W2950671516","https://openalex.org/W2950993016","https://openalex.org/W2951160681","https://openalex.org/W2967125766","https://openalex.org/W2982531601","https://openalex.org/W2983351185","https://openalex.org/W2990618091","https://openalex.org/W3011218362","https://openalex.org/W3058159016","https://openalex.org/W3105109544"],"related_works":["https://openalex.org/W2002723386","https://openalex.org/W2749851556","https://openalex.org/W2765793069","https://openalex.org/W2550586733","https://openalex.org/W4200050032","https://openalex.org/W2515795842","https://openalex.org/W2324462508","https://openalex.org/W1855401909","https://openalex.org/W3138936383","https://openalex.org/W2601089939"],"abstract_inverted_index":{"Accurate":[0],"and":[1,16,36,78,104,148,180,230,240,253],"sensitive":[2],"taxonomic":[3,56,100,157,207],"profiling":[4],"is":[5,25,125,251],"essential":[6],"for":[7,17,55,76,95,98,135,206],"any":[8],"metagenomic":[9,137,197],"analysis":[10,129],"to":[11,109,121,162,168,218],"reveal":[12],"microbial":[13],"community":[14],"structure":[15],"potential":[18],"functional":[19],"prediction.":[20],"Antimicrobial":[21],"resistance":[22],"(AMR)":[23],"detection":[24,77,105,134],"also":[26,210],"a":[27,83,126],"critical":[28],"task":[29],"in":[30,82],"the":[31,49,110,119,170,195,227,232,238],"clinical":[32],"diagnosis":[33],"of":[34,52,102,106,172,222,243],"infection":[35],"antimicrobial":[37],"therapy.":[38],"By":[39],"incorporating":[40],"Oxford":[41],"Nanopore":[42],"Technologies":[43],"(ONT)":[44],"sequencing,":[45],"users":[46],"benefit":[47],"from":[48],"high-confidence":[50],"alignment":[51,178],"long":[53],"reads":[54,91,150],"classification,":[57],"even":[58],"among":[59],"bacteria":[60],"with":[61,70,131,159,164],"similar":[62],"genomes.":[63],"Portable":[64],"ONT":[65,89,136],"devices,":[66],"such":[67],"as":[68],"VolTRAX":[69],"MinION,":[71],"allow":[72],"short":[73],"turnaround":[74],"time":[75],"can":[79],"be":[80],"used":[81],"lightweight":[84],"laboratory":[85],"setting.":[86],"However,":[87],"error-prone":[88],"sequencing":[90,138],"are":[92],"still":[93],"challenging":[94],"existing":[96,204],"software":[97,130,205],"accurate":[99,229],"classification":[101,158],"microbes":[103],"AMR":[107,133,185,189,223,244],"down":[108,161],"drug":[111,239],"level.":[112],"In":[113,191],"this":[114],"paper,":[115],"we":[116],"present":[117],"MegaPath-Nano,":[118],"successor":[120],"NGS-based":[122],"MegaPath.":[123],"It":[124],"high-precision":[127],"compositional":[128],"drug-level":[132,184],"data.":[139],"MegaPath-Nano":[140,199,225,250],"performs":[141],"1)":[142],"thorough":[143],"multi-level":[144],"filtering":[145],"against":[146,246],"decoy":[147],"human":[149],"while":[151],"removing":[152],"noisy":[153],"alignments,":[154,174],"2)":[155],"alignment-based":[156],"RefSeq":[160],"strain-level,":[163],"an":[165],"alignment-reassignment":[166],"algorithm":[167],"tackle":[169],"challenge":[171],"non-unique":[173],"based":[175],"on":[176],"global":[177],"distribution,":[179],"3)":[181],"comprehensive":[182,234],"downstream":[183],"detection,":[186],"integrating":[187],"five":[188,212],"databases.":[190],"our":[192],"benchmarks":[193],"using":[194,216],"Zymo":[196],"dataset,":[198],"performed":[200],"better":[201],"than":[202],"other":[203,247],"classification.":[208],"We":[209],"sequenced":[211],"real":[213],"patient":[214],"isolates":[215],"MinION":[217],"benchmark":[219],"its":[220],"performance":[221],"detection.":[224],"was":[226],"most":[228,233],"provided":[231],"output":[235],"at":[236,255],"both":[237],"class":[241],"level":[242],"prediction":[245],"state-of-the-art":[248],"software.":[249],"open-source":[252],"available":[254],"https://github.com/HKU-BAL/MegaPath-Nano.":[256]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
