{"id":"https://openalex.org/W2802977902","doi":"https://doi.org/10.1007/s40484-018-0132-y","title":"BMTK: a toolkit for determining modules in biological bipartite networks","display_name":"BMTK: a toolkit for determining modules in biological bipartite networks","publication_year":2018,"publication_date":"2018-05-07","ids":{"openalex":"https://openalex.org/W2802977902","doi":"https://doi.org/10.1007/s40484-018-0132-y","mag":"2802977902"},"language":"en","primary_location":{"id":"doi:10.1007/s40484-018-0132-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-018-0132-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-018-0132-y.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1007/s40484-018-0132-y.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100349955","display_name":"Bei Wang","orcid":"https://orcid.org/0000-0002-8931-430X"},"institutions":[{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bei Wang","raw_affiliation_strings":["NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","institution_ids":["https://openalex.org/I4210120485"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China","institution_ids":["https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100730361","display_name":"Jinyu Chen","orcid":"https://orcid.org/0000-0001-9790-998X"},"institutions":[{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyu Chen","raw_affiliation_strings":["NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","institution_ids":["https://openalex.org/I4210120485"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China","institution_ids":["https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076619069","display_name":"Shihua Zhang","orcid":"https://orcid.org/0000-0003-0192-7118"},"institutions":[{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shihua Zhang","raw_affiliation_strings":["NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China","institution_ids":["https://openalex.org/I4210120485"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China","institution_ids":["https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1990,"currency":"USD","value_usd":1990},"apc_paid":{"value":1990,"currency":"USD","value_usd":1990},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03624306,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"2","first_page":"186","last_page":"192"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9944000244140625,"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/bipartite-graph","display_name":"Bipartite graph","score":0.9349098205566406},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8027507066726685},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6448187828063965},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6253216862678528},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6243718266487122},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5027210712432861},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4846392273902893},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4181118607521057},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37284547090530396},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21116873621940613},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.10784158110618591},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.09686943888664246},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08256390690803528}],"concepts":[{"id":"https://openalex.org/C197657726","wikidata":"https://www.wikidata.org/wiki/Q174733","display_name":"Bipartite graph","level":3,"score":0.9349098205566406},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8027507066726685},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6448187828063965},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6253216862678528},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6243718266487122},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5027210712432861},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4846392273902893},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4181118607521057},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37284547090530396},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21116873621940613},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.10784158110618591},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.09686943888664246},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08256390690803528},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s40484-018-0132-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-018-0132-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-018-0132-y.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s40484-018-0132-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-018-0132-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-018-0132-y.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1113985643","display_name":null,"funder_award_id":"QYZDB-SSW-SYS008","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G2897020631","display_name":null,"funder_award_id":"61422309","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2953583009","display_name":null,"funder_award_id":"XDB13040600","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3523307272","display_name":null,"funder_award_id":"61621003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4332384139","display_name":null,"funder_award_id":"XDB13040600","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G7536008178","display_name":null,"funder_award_id":"11661141019.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8217650542","display_name":null,"funder_award_id":"61379092","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2802977902.pdf","grobid_xml":"https://content.openalex.org/works/W2802977902.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1584510240","https://openalex.org/W1866364567","https://openalex.org/W1987643017","https://openalex.org/W2001554877","https://openalex.org/W2024722675","https://openalex.org/W2032273054","https://openalex.org/W2067803871","https://openalex.org/W2067841476","https://openalex.org/W2070040136","https://openalex.org/W2082565035","https://openalex.org/W2085658677","https://openalex.org/W2086805702","https://openalex.org/W2096578372","https://openalex.org/W2096967557","https://openalex.org/W2108812454","https://openalex.org/W2121365413","https://openalex.org/W2125673723","https://openalex.org/W2133102806","https://openalex.org/W2151936673","https://openalex.org/W2153838454","https://openalex.org/W2153840021","https://openalex.org/W2156341654","https://openalex.org/W2159675211","https://openalex.org/W2160249427","https://openalex.org/W2162172965","https://openalex.org/W2162928287","https://openalex.org/W2165533101","https://openalex.org/W2165891030","https://openalex.org/W2168764383","https://openalex.org/W2168768094","https://openalex.org/W2962770299"],"related_works":["https://openalex.org/W2371352078","https://openalex.org/W2953461625","https://openalex.org/W2077383796","https://openalex.org/W2080136900","https://openalex.org/W2372768926","https://openalex.org/W2999799752","https://openalex.org/W2054458431","https://openalex.org/W3013576436","https://openalex.org/W2286030698","https://openalex.org/W3088754131"],"abstract_inverted_index":{"Background":[0],"Module":[1],"detection":[2,27],"is":[3,28,50,131],"widely":[4],"used":[5],"to":[6,21,93,107],"analyze":[7],"and":[8,16,34,39,81,86,89],"visualize":[9],"biological":[10,37,125],"networks.":[11,126],"A":[12],"number":[13],"of":[14,137],"methods":[15,42],"tools":[17],"have":[18,43],"been":[19,44],"developed":[20,45],"achieve":[22],"it.":[23,47],"Meanwhile,":[24],"bipartite":[25,36,105,120,124],"module":[26],"also":[29,98],"very":[30],"useful":[31],"for":[32,46,54,118],"mining":[33],"analyzing":[35],"networks":[38],"a":[40,77,103,115],"few":[41,51],"However,":[48],"there":[49],"user\u2010friendly":[52],"toolkit":[53,66,101],"this":[55,59,100],"task.":[56],"Methods":[57],"To":[58],"end,":[60],"we":[61],"develop":[62],"an":[63],"online":[64],"web":[65,129],"BMTK,":[67],"which":[68],"implements":[69],"seven":[70],"existing":[71],"methods.":[72],"Results":[73],"BMTK":[74,112],"provide":[75],"s":[76],"uniform":[78],"operation":[79],"platform":[80],"visualization":[82],"function,":[83],"standardizes":[84],"input":[85],"output":[87],"format,":[88],"improves":[90],"algorithmic":[91],"structure":[92],"enhance":[94],"computing":[95],"speed.":[96],"We":[97],"apply":[99],"onto":[102],"drug\u2010target":[104],"network":[106],"demonstrate":[108],"its":[109],"effectiveness.":[110],"Conclusions":[111],"will":[113],"be":[114],"powerful":[116],"tool":[117],"detecting":[119],"modules":[121],"in":[122],"diverse":[123],"Availability:":[127],"The":[128],"application":[130],"freely":[132],"accessible":[133],"at":[134],"the":[135],"website":[136],"Zhang":[138],"lab.":[139]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}