{"id":"https://openalex.org/W2209496154","doi":"https://doi.org/10.1109/bibm.2015.7359679","title":"Identification of phenotypic networks based on whole transcriptome by comparative network decomposition","display_name":"Identification of phenotypic networks based on whole transcriptome by comparative network decomposition","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2209496154","doi":"https://doi.org/10.1109/bibm.2015.7359679","mag":"2209496154"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359679","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359679","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/A5023728748","display_name":"Chuanchao Zhang","orcid":"https://orcid.org/0000-0003-0690-613X"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chuanchao Zhang","raw_affiliation_strings":["Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China","Schocl of Computer, Wuhan University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"Schocl of Computer, Wuhan University, Wuhan, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070214802","display_name":"Juan Liu","orcid":"https://orcid.org/0000-0002-1115-6380"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juan Liu","raw_affiliation_strings":["Schocl of Computer, Wuhan University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"Schocl of Computer, Wuhan University, Wuhan, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058311447","display_name":"Qianqian Shi","orcid":"https://orcid.org/0000-0002-5266-6731"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianqian Shi","raw_affiliation_strings":["Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, Shanghai, CN"],"affiliations":[{"raw_affiliation_string":"Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, Shanghai, CN","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026321844","display_name":"Tao Zeng","orcid":"https://orcid.org/0000-0002-0295-3994"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Zeng","raw_affiliation_strings":["Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012283696","display_name":"Luonan Chen","orcid":"https://orcid.org/0000-0002-3960-0068"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luonan Chen","raw_affiliation_strings":["Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5023728748"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I37461747"],"apc_list":null,"apc_paid":null,"fwci":0.1459,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56230284,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"32","issue":null,"first_page":"189","last_page":"194"},"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":0.9980000257492065,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.994700014591217,"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/phenotype","display_name":"Phenotype","score":0.6974616050720215},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6853698492050171},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6248655319213867},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5404753088951111},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5188218951225281},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5167197585105896},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5154412984848022},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4949316382408142},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4782218635082245},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4396594762802124},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4393860101699829},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25577855110168457},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1784386932849884}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.6974616050720215},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6853698492050171},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6248655319213867},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5404753088951111},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5188218951225281},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5167197585105896},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5154412984848022},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4949316382408142},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4782218635082245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4396594762802124},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4393860101699829},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25577855110168457},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1784386932849884},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359679","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359679","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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W23729838","https://openalex.org/W1527927437","https://openalex.org/W1994803330","https://openalex.org/W1996086117","https://openalex.org/W2011986160","https://openalex.org/W2029115700","https://openalex.org/W2072103747","https://openalex.org/W2079031049","https://openalex.org/W2081930221","https://openalex.org/W2093559498","https://openalex.org/W2101268659","https://openalex.org/W2103017472","https://openalex.org/W2110265246","https://openalex.org/W2122863289","https://openalex.org/W2130410032","https://openalex.org/W2130809861","https://openalex.org/W2143166200","https://openalex.org/W2146561547","https://openalex.org/W2166089858","https://openalex.org/W2171108134","https://openalex.org/W2171662214","https://openalex.org/W4235025907"],"related_works":["https://openalex.org/W1411590778","https://openalex.org/W2158714033","https://openalex.org/W4386628104","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4206945140","https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W2509687359"],"abstract_inverted_index":{"Complex":[0],"diseases":[1,249],"are":[2],"usually":[3],"caused":[4],"by":[5,95],"the":[6,9,20,48,152,178,196,205,213,244],"dysfunctions":[7],"of":[8,47,85,110,151,193,198,247],"molecular":[10,13],"system":[11,49],"or":[12,54],"network":[14,27,41,77,100,132],"rather":[15,156],"than":[16,157],"individual":[17],"molecules.":[18],"Generally,":[19],"conventional":[21,158],"methods":[22],"first":[23],"obtain":[24],"a":[25,40,45,51,65,136,166,225,237],"disease-associated":[26],"based":[28,68],"on":[29,69,119],"expression":[30],"data":[31],"and":[32,87,91,101,116,122,180,201,207,217,234,240,243],"then":[33],"study":[34,168,246],"its":[35,255],"biological":[36,52,138,215],"functions.":[37,59],"However,":[38],"such":[39],"may":[42,55],"be":[43],"only":[44,160],"part":[46],"facilitating":[50],"function":[53],"involve":[56],"in":[57,236],"multiple":[58,149],"In":[60,195],"this":[61],"paper,":[62],"we":[63],"present":[64],"computational":[66],"framework":[67],"an":[70],"integer":[71],"programming":[72],"model,":[73],"named":[74],"as":[75],"comparative":[76,245],"decomposition":[78],"(CND),":[79],"to":[80,124,135,169,176],"jointly":[81],"identify":[82,148,177],"optimal":[83,93],"structures":[84],"significant":[86,162,179,208],"moderate":[88,181,206],"phenotypic":[89,127,131,154,163,182,209],"functions/networks":[90],"their":[92,218],"combination":[94],"integrating":[96],"gene":[97,99,102,120],"expression,":[98],"ontology":[103],"together.":[104],"Particularly,":[105],"CND":[106,146,172,222],"makes":[107],"full":[108],"use":[109],"dysfunctional":[111],"information,":[112],"e.g.":[113,191],"both":[114],"strong":[115],"weak":[117],"changes":[118],"expressions":[121],"correlations,":[123],"extract":[125],"various":[126],"networks,":[128,155],"where":[129],"one":[130],"just":[133],"corresponds":[134],"specific":[137],"function.":[139],"A":[140],"synthetic":[141],"example":[142],"clearly":[143],"suggests":[144],"that":[145],"can":[147,211,230],"types":[150],"disease-related":[153,214],"approaches":[159],"exact":[161],"networks.":[164,220],"As":[165],"proof-of-concept":[167],"real":[170],"data,":[171],"is":[173,223],"further":[174],"used":[175],"networks":[183,210,235],"for":[184],"discriminating":[185],"two":[186],"different":[187],"but":[188],"associated":[189],"diseases,":[190],"subtypes":[192],"diabetes.":[194],"comparison":[197],"type":[199,202],"1":[200],"2":[203],"diabetes,":[204],"capture":[212],"functions":[216],"corresponding":[219],"Therefore,":[221],"actually":[224],"powerful":[226],"bioinformatics":[227],"tool,":[228],"which":[229],"investigate":[231],"phenotype-associated":[232],"genes":[233],"whole":[238],"transcriptome":[239],"function-centered":[241],"manner,":[242],"complex":[248],"with":[250],"other":[251],"works":[252],"also":[253],"demonstrates":[254],"effectiveness.":[256]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}