{"id":"https://openalex.org/W2210883998","doi":"https://doi.org/10.1109/bibm.2015.7359675","title":"Reconstructing directed gene regulatory network by only gene expression data","display_name":"Reconstructing directed gene regulatory network by only gene expression data","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2210883998","doi":"https://doi.org/10.1109/bibm.2015.7359675","mag":"2210883998"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359675","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359675","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 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/A5100388624","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0002-2794-7371"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"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":"Lu Zhang","raw_affiliation_strings":["Department of Computer Science City, University of Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science City, University of Hong Kong","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047448762","display_name":"Yen Kaow Ng","orcid":"https://orcid.org/0000-0003-1556-9438"},"institutions":[{"id":"https://openalex.org/I931681460","display_name":"Universiti Tunku Abdul Rahman","ror":"https://ror.org/050pq4m56","country_code":"MY","type":"education","lineage":["https://openalex.org/I931681460"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Yen Kaow Ng","raw_affiliation_strings":["Department of Computer Science, Universiti Tunku Abdul, Rahman, Malaysia"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universiti Tunku Abdul, Rahman, Malaysia","institution_ids":["https://openalex.org/I931681460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083428910","display_name":"Shuai Cheng Li","orcid":"https://orcid.org/0000-0001-6246-6349"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"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":"ShuaiCheng Li","raw_affiliation_strings":["Department of Computer Science City, University of Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science City, University of Hong Kong","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100388624"],"corresponding_institution_ids":["https://openalex.org/I168719708","https://openalex.org/I889458895"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.07262483,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"25","issue":null,"first_page":"163","last_page":"170"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10885","display_name":"Gene expression and cancer classification","score":0.9957000017166138,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7435744404792786},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6838408708572388},{"id":"https://openalex.org/keywords/expression-quantitative-trait-loci","display_name":"Expression quantitative trait loci","score":0.6393365859985352},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.595954418182373},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.573853075504303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5620187520980835},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.45493894815444946},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4380491077899933},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43045830726623535},{"id":"https://openalex.org/keywords/gene-co-expression-network","display_name":"Gene co-expression network","score":0.4207955300807953},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39954620599746704},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3442750573158264},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3186452090740204},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3059716820716858},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.28733545541763306},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2750869393348694}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7435744404792786},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6838408708572388},{"id":"https://openalex.org/C168393362","wikidata":"https://www.wikidata.org/wiki/Q5421706","display_name":"Expression quantitative trait loci","level":5,"score":0.6393365859985352},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.595954418182373},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.573853075504303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5620187520980835},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.45493894815444946},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4380491077899933},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43045830726623535},{"id":"https://openalex.org/C2778022302","wikidata":"https://www.wikidata.org/wiki/Q18207329","display_name":"Gene co-expression network","level":5,"score":0.4207955300807953},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39954620599746704},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3442750573158264},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3186452090740204},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3059716820716858},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.28733545541763306},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2750869393348694},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359675","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359675","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1551305907","https://openalex.org/W1607556721","https://openalex.org/W1964040105","https://openalex.org/W1968291759","https://openalex.org/W1979700602","https://openalex.org/W1984785521","https://openalex.org/W1991458316","https://openalex.org/W1994889847","https://openalex.org/W2008395997","https://openalex.org/W2033105784","https://openalex.org/W2044525257","https://openalex.org/W2060475443","https://openalex.org/W2076513103","https://openalex.org/W2106555403","https://openalex.org/W2110265246","https://openalex.org/W2118258530","https://openalex.org/W2120280233","https://openalex.org/W2129265801","https://openalex.org/W2136940727","https://openalex.org/W2150729756","https://openalex.org/W2152227081","https://openalex.org/W2161732139","https://openalex.org/W2163296115","https://openalex.org/W2171118759","https://openalex.org/W2325321733","https://openalex.org/W2724303067","https://openalex.org/W3099289621","https://openalex.org/W4239414011","https://openalex.org/W6739988322"],"related_works":["https://openalex.org/W3012307849","https://openalex.org/W2020355323","https://openalex.org/W2010571965","https://openalex.org/W2602141149","https://openalex.org/W2002709996","https://openalex.org/W3128451840","https://openalex.org/W4387092964","https://openalex.org/W2103471012","https://openalex.org/W2966064480","https://openalex.org/W2115810854"],"abstract_inverted_index":{"Accurately":[0],"identifying":[1],"gene":[2,27,51,88,98],"regulatory":[3,35,89,94],"network":[4,19,39,147],"serves":[5],"an":[6],"important":[7,135,155],"task":[8],"in":[9,11,37,137,145],"understanding":[10],"vivo":[12],"biological":[13],"activities.":[14],"The":[15],"inference":[16],"of":[17,26,44],"such":[18],"is":[20,84],"often":[21],"accomplished":[22],"through":[23,50],"the":[24,34,38,42,65,93,127,146],"use":[25],"expression":[28,99],"data.":[29,100],"Some":[30],"methods":[31],"further":[32],"predict":[33],"directions":[36],"by":[40],"using":[41],"location":[43],"eQTL":[45],"single":[46],"nucleotide":[47],"polymorphisms,":[48],"or":[49],"knock":[52],"out/down":[53],"experiments;":[54],"regrettably,":[55],"these":[56],"additional":[57],"data":[58,104],"are":[59],"not":[60],"always":[61],"available,":[62],"especially":[63],"for":[64,160],"samples":[66],"deriving":[67],"from":[68,96],"human":[69,161],"tissues.":[70],"In":[71,117],"this":[72],"paper,":[73],"we":[74],"propose":[75],"Context":[76],"Based":[77],"Dependency":[78],"Network":[79],"(CBDN),":[80],"a":[81,138],"method":[82],"that":[83],"able":[85],"to":[86,108,133,149],"infer":[87],"networks,":[90],"complete":[91],"with":[92,120],"directions,":[95],"only":[97],"CBDN":[101,125,140],"applies":[102],"directed":[103],"processing":[105],"inequality":[106],"(DDPI)":[107],"distinguish":[109],"between":[110,115],"direct":[111],"and":[112,122,158],"transitive":[113],"relationship":[114],"genes.":[116],"our":[118],"experiments":[119],"simulated":[121],"real":[123],"data,":[124],"outperforms":[126],"current":[128],"state-of-the-art":[129],"approaches.":[130],"When":[131],"used":[132],"identify":[134],"regulators":[136,156],"network,":[139],"1.":[141],"correctly":[142],"identified":[143],"TYROBP":[144],"related":[148],"Alzheimer's":[150],"disease;":[151],"2.":[152],"predicted":[153],"potential":[154],"ZNF329":[157],"RB1":[159],"brain":[162],"tumors.":[163]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
