{"id":"https://openalex.org/W1979360205","doi":"https://doi.org/10.1186/1752-0509-7-s4-s3","title":"A scalable method for discovering significant subnetworks","display_name":"A scalable method for discovering significant subnetworks","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W1979360205","doi":"https://doi.org/10.1186/1752-0509-7-s4-s3","mag":"1979360205","pmid":"https://pubmed.ncbi.nlm.nih.gov/24565174"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-7-s4-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-s4-s3","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-S4-S3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-S4-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101608475","display_name":"Md Mahmudul Hasan","orcid":"https://orcid.org/0000-0003-2543-3112"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Md Mahmudul Hasan","raw_affiliation_strings":["Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","Computer and Information Science and Engineering, University of Florida, , USA"],"affiliations":[{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, , USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106133937","display_name":"Yusuf Kavurucu","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I157637111","display_name":"Naval Academy","ror":"https://ror.org/05syseh24","country_code":"TR","type":"education","lineage":["https://openalex.org/I157637111"]}],"countries":["TR","US"],"is_corresponding":false,"raw_author_name":"Yusuf Kavurucu","raw_affiliation_strings":["Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","Turkish Naval Academy, Istanbul, Turkey","Computer and Information Science and Engineering, University of Florida, USA"],"affiliations":[{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Turkish Naval Academy, Istanbul, Turkey","institution_ids":["https://openalex.org/I157637111"]},{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","Computer and Information Science and Engineering, University of Florida, , USA"],"affiliations":[{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, FL, 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Computer and Information Science and Engineering, University of Florida, , USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101608475"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.4492,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64669326,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"7","issue":"Suppl 4","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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":0.9887999892234802,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.918338418006897},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7212603092193604},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6832347512245178},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6575539112091064},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6249459981918335},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.6005290746688843},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.45498859882354736},{"id":"https://openalex.org/keywords/prokaryote","display_name":"Prokaryote","score":0.43510347604751587},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.42596572637557983},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4249211251735687},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42313557863235474},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.417688250541687},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35285788774490356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.24574363231658936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23311644792556763},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.11951747536659241},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1172177791595459}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.918338418006897},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7212603092193604},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6832347512245178},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6575539112091064},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6249459981918335},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.6005290746688843},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.45498859882354736},{"id":"https://openalex.org/C2780918051","wikidata":"https://www.wikidata.org/wiki/Q19081","display_name":"Prokaryote","level":3,"score":0.43510347604751587},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.42596572637557983},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4249211251735687},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42313557863235474},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.417688250541687},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35285788774490356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.24574363231658936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23311644792556763},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.11951747536659241},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1172177791595459},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-7-s4-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-s4-s3","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-S4-S3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:24565174","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24565174","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:2847695","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3854656","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:10.1186/1752-0509-7-s4-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-s4-s3","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-S4-S3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1047034216","display_name":"EMT/BSSE: Biological networks as a communication model for entities with complex interactions","funder_award_id":"0829867","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2593556431","display_name":"CAREER: New Technologies for Querying Pathway Databases","funder_award_id":"0845439","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8923045389","display_name":null,"funder_award_id":"IIS-0845439","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1979360205.pdf","grobid_xml":"https://content.openalex.org/works/W1979360205.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1490787220","https://openalex.org/W1499476884","https://openalex.org/W1510585142","https://openalex.org/W1529898704","https://openalex.org/W1605319014","https://openalex.org/W1644749979","https://openalex.org/W1850739480","https://openalex.org/W1970259423","https://openalex.org/W2031539502","https://openalex.org/W2033459252","https://openalex.org/W2036265926","https://openalex.org/W2057488525","https://openalex.org/W2102039273","https://openalex.org/W2110503722","https://openalex.org/W2118349699","https://openalex.org/W2119740363","https://openalex.org/W2124996875","https://openalex.org/W2126969584","https://openalex.org/W2141146725","https://openalex.org/W2146771637","https://openalex.org/W2152613879","https://openalex.org/W2153624566","https://openalex.org/W2159482845","https://openalex.org/W2160556205","https://openalex.org/W2162481448","https://openalex.org/W2168209541","https://openalex.org/W2170726034","https://openalex.org/W2400499165","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2028552635","https://openalex.org/W2478888221","https://openalex.org/W2095452756","https://openalex.org/W2155492529","https://openalex.org/W15348386","https://openalex.org/W4252504573","https://openalex.org/W2521885831","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W2494457055"],"abstract_inverted_index":{"Experiments":[0],"on":[1,66,90],"comprehensive":[2],"data":[3,29,50,75,110],"sets":[4,51],"depict":[5],"that":[6,33,118],"the":[7,67,70,73,77,91],"most":[8],"probable":[9],"subnetworks":[10,34,53],"found":[11,32],"by":[12],"SiS":[13,44,81,112],"in":[14,35,72,103],"a":[15,84,114],"large":[16,49,115],"collection":[17],"of":[18,42,57,69,80,122],"networks":[19],"are":[20,37],"also":[21,45],"very":[22],"frequent":[23],"as":[24],"well.":[25],"In":[26,105],"metabolic":[27],"network":[28,109],"set,":[30,76,111],"we":[31],"eukaryote":[36],"more":[38],"conserved":[39],"than":[40,60],"those":[41],"prokaryote.":[43],"scales":[46],"well":[47],"to":[48,87],"and":[52,54],"runs":[55,94],"orders":[56],"magnitude":[58],"faster":[59],"an":[61],"existing":[62],"method,":[63],"MULE.":[64],"Depending":[65],"size":[68],"subnetwork":[71,117],"same":[74],"running":[78],"time":[79],"ranges":[82],"from":[83],"few":[85],"seconds":[86],"minutes;":[88],"MULE,":[89],"other":[92],"hand,":[93],"either":[95],"for":[96],"hours":[97],"or":[98],"does":[99],"not":[100],"even":[101],"finish":[102],"days.":[104],"human":[106],"transcription":[107],"regulatory":[108],"finds":[113],"backbone":[116],"appears":[119],"frequently":[120],"regardless":[121],"diverse":[123],"cell":[124],"types.":[125]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
