{"id":"https://openalex.org/W2139827982","doi":"https://doi.org/10.1186/1756-0381-7-16","title":"Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets","display_name":"Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets","publication_year":2014,"publication_date":"2014-08-18","ids":{"openalex":"https://openalex.org/W2139827982","doi":"https://doi.org/10.1186/1756-0381-7-16","mag":"2139827982","pmid":"https://pubmed.ncbi.nlm.nih.gov/25221624"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-7-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-7-16","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-7-16","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-7-16","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091100480","display_name":"Saeed Salem","orcid":"https://orcid.org/0000-0001-6478-4674"},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Saeed Salem","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, ND 58102, USA","[Department of Computer Science, North Dakota State University, Fargo, ND 58102, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, ND 58102, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"[Department of Computer Science, North Dakota State University, Fargo, ND 58102, USA]","institution_ids":["https://openalex.org/I57328836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039408873","display_name":"Cagri Ozcaglar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cagri Ozcaglar","raw_affiliation_strings":["Amazon, Seattle, WA 98101, USA"],"affiliations":[{"raw_affiliation_string":"Amazon, Seattle, WA 98101, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091100480"],"corresponding_institution_ids":["https://openalex.org/I57328836"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2843,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.60729872,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"7","issue":"1","first_page":"16","last_page":"16"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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":0.9904999732971191,"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/spurious-relationship","display_name":"Spurious relationship","score":0.6990492343902588},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6646888852119446},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.607526957988739},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5494123101234436},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5268344283103943},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5040789842605591},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48042893409729004},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47657132148742676},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.42114120721817017},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.41841840744018555},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3963485658168793},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3650761544704437},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.31759387254714966},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26103246212005615},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22497716546058655},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1969616413116455},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.19557860493659973},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.17127808928489685},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.15068009495735168},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.12495201826095581}],"concepts":[{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.6990492343902588},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6646888852119446},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.607526957988739},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5494123101234436},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5268344283103943},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5040789842605591},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48042893409729004},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47657132148742676},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.42114120721817017},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.41841840744018555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3963485658168793},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3650761544704437},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.31759387254714966},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26103246212005615},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22497716546058655},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1969616413116455},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.19557860493659973},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.17127808928489685},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.15068009495735168},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.12495201826095581},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1756-0381-7-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-7-16","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-7-16","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:25221624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25221624","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4151083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4151083","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-7-16","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-7-16","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-7-16","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G4062762668","display_name":null,"funder_award_id":"P20 GM103442","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5698253053","display_name":null,"funder_award_id":"P20 RR016471","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G7231804310","display_name":null,"funder_award_id":"GM103442","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139827982.pdf","grobid_xml":"https://content.openalex.org/works/W2139827982.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W287282549","https://openalex.org/W333587792","https://openalex.org/W1783384641","https://openalex.org/W1979360205","https://openalex.org/W1991395536","https://openalex.org/W2002850151","https://openalex.org/W2025897051","https://openalex.org/W2027770225","https://openalex.org/W2034784092","https://openalex.org/W2096281132","https://openalex.org/W2106650313","https://openalex.org/W2110620844","https://openalex.org/W2112811019","https://openalex.org/W2116961371","https://openalex.org/W2126969584","https://openalex.org/W2132914434","https://openalex.org/W2133465414","https://openalex.org/W2136850043","https://openalex.org/W2144317357","https://openalex.org/W2145704518","https://openalex.org/W2154947819","https://openalex.org/W2158217645","https://openalex.org/W2160556205","https://openalex.org/W2166994421","https://openalex.org/W2291822716","https://openalex.org/W2491844331","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2009966535","https://openalex.org/W3135849929","https://openalex.org/W4205963003","https://openalex.org/W1488437289","https://openalex.org/W2748644580","https://openalex.org/W2352070969","https://openalex.org/W2762277149","https://openalex.org/W2001670874","https://openalex.org/W2390847229","https://openalex.org/W2139827982"],"abstract_inverted_index":{"We":[0],"propose":[1],"a":[2,8,33],"joint":[3],"mining":[4],"algorithm":[5],"that":[6,69],"constructs":[7],"weighted":[9,51],"hybrid":[10,30,52],"similarity":[11,53],"graph":[12,31,54],"whose":[13],"nodes":[14],"are":[15,73],"the":[16,37,44,50,70],"coexpression":[17,26,47,57],"links.":[18,48],"The":[19],"weight":[20],"of":[21,36,43],"an":[22],"edge":[23],"between":[24],"two":[25,46],"links":[27],"in":[28],"this":[29],"is":[32],"linear":[34],"combination":[35],"topological":[38],"similarities":[39,42],"and":[40,86],"co-appearance":[41],"corresponding":[45],"Clustering":[49],"yields":[55],"recurrent":[56],"link":[58],"clusters":[59],"(modules).":[60],"Experimental":[61],"results":[62],"on":[63],"Human":[64],"gene":[65],"expression":[66],"datasets":[67],"show":[68],"reported":[71],"modules":[72],"functionally":[74],"homogeneous":[75],"as":[76],"evident":[77],"by":[78],"their":[79],"enrichment":[80],"with":[81],"biological":[82],"process":[83],"GO":[84],"terms":[85],"KEGG":[87],"pathways.":[88]},"counts_by_year":[{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-14T08:43:22.919905","created_date":"2025-10-10T00:00:00"}
