{"id":"https://openalex.org/W2204438866","doi":"https://doi.org/10.1109/bibm.2015.7359852","title":"On the comparison of state- and transition-based analysis of biological relevance in gene co-expression networks","display_name":"On the comparison of state- and transition-based analysis of biological relevance in gene co-expression networks","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2204438866","doi":"https://doi.org/10.1109/bibm.2015.7359852","mag":"2204438866"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359852","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359852","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/A5036687490","display_name":"Kathryn Cooper","orcid":"https://orcid.org/0000-0002-6341-9648"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kathryn Cooper","raw_affiliation_strings":["College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027386429","display_name":"Prasuna Vemuri","orcid":null},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Prasuna Vemuri","raw_affiliation_strings":["College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047703641","display_name":"Hesham Ali","orcid":"https://orcid.org/0000-0001-6675-7987"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hesham Ali","raw_affiliation_strings":["College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE","institution_ids":["https://openalex.org/I122266389"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036687490"],"corresponding_institution_ids":["https://openalex.org/I122266389"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07056486,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"327","issue":null,"first_page":"1197","last_page":"1203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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":0.9876999855041504,"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/relevance","display_name":"Relevance (law)","score":0.7503362894058228},{"id":"https://openalex.org/keywords/transition","display_name":"Transition (genetics)","score":0.5470869541168213},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5222288370132446},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5011909008026123},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4978032112121582},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4919905364513397},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.456648051738739},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3362152576446533},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23303836584091187},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2144363522529602},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.11502233147621155},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.07045727968215942}],"concepts":[{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.7503362894058228},{"id":"https://openalex.org/C194232998","wikidata":"https://www.wikidata.org/wiki/Q1606712","display_name":"Transition (genetics)","level":3,"score":0.5470869541168213},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5222288370132446},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5011909008026123},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4978032112121582},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4919905364513397},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.456648051738739},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3362152576446533},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23303836584091187},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2144363522529602},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.11502233147621155},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.07045727968215942},{"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359852","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359852","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":22,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1783384641","https://openalex.org/W1971421925","https://openalex.org/W1982413833","https://openalex.org/W1989119979","https://openalex.org/W1989921625","https://openalex.org/W2008620264","https://openalex.org/W2040956707","https://openalex.org/W2059747434","https://openalex.org/W2063198633","https://openalex.org/W2108345226","https://openalex.org/W2115505574","https://openalex.org/W2128623429","https://openalex.org/W2133102806","https://openalex.org/W2160313295","https://openalex.org/W2163480486","https://openalex.org/W2328323965","https://openalex.org/W2395165997","https://openalex.org/W2406873073","https://openalex.org/W2952482610","https://openalex.org/W6608852248","https://openalex.org/W6711529987"],"related_works":["https://openalex.org/W2085384747","https://openalex.org/W2088166309","https://openalex.org/W1891216533","https://openalex.org/W4312133475","https://openalex.org/W4238976562","https://openalex.org/W2276587472","https://openalex.org/W2615795876","https://openalex.org/W2049612369","https://openalex.org/W2770872919","https://openalex.org/W4214571255"],"abstract_inverted_index":{"Traditional":[0],"correlation":[1],"network":[2,8,21,59,212,231],"analysis":[3,127],"typically":[4,228],"involves":[5],"creating":[6],"a":[7,38,52,170,220,238],"using":[9,211],"gene":[10,137],"expression":[11,138],"data":[12,139],"and":[13,74,151,153,192,210],"then":[14,72],"identifying":[15],"biologically":[16],"relevant":[17],"clusters":[18],"from":[19,140,244],"that":[20,113,219],"by":[22,57],"enrichment":[23,89,163],"with":[24,237],"Gene":[25],"Ontology":[26],"or":[27,48,223],"pathway":[28],"information.":[29],"When":[30],"one":[31],"wants":[32],"to":[33,94,118,159,241,247],"examine":[34,80],"these":[35,69,97],"networks":[36,84],"in":[37,92,215,230,245,248],"dynamic":[39,120,161,193],"way":[40],"-":[41,51,218],"such":[42],"as":[43],"between":[44,190],"controls":[45],"versus":[46],"treatment":[47],"over":[49],"time":[50,63,147],"\u201csnapshot\u201d":[53,83],"approach":[54,158,172,227,240],"is":[55,112],"taken":[56],"comparing":[58],"structures":[60,70],"at":[61,144],"each":[62],"point.":[64],"The":[65,182],"biological":[66,129,180,198],"relevance":[67],"of":[68,90,128,178,184,226,251],"are":[71],"reported":[73],"compared.":[75],"In":[76,165],"this":[77,133,166,185],"research,":[78],"we":[79,135,168],"the":[81,88,104,141,155,160],"same":[82],"but":[85],"focus":[86],"on":[87],"changes":[91],"structure":[93,194],"determine":[95],"if":[96],"results":[98,183,201],"give":[99],"any":[100],"more":[101,114],"insight":[102],"into":[103],"mechanisms":[105],"behind":[106],"observed":[107],"phenotypes.":[108],"Our":[109],"main":[110],"hypothesis":[111],"information,":[115],"particularly":[116],"related":[117],"potential":[119],"changes,":[121],"can":[122,234],"be":[123,235],"obtained":[124],"through":[125,197],"transition-based":[126,162],"networks.":[130,181],"To":[131],"test":[132],"hypothesis,":[134],"compare":[136,154],"mouse":[142],"hippocampus":[143],"three":[145],"different":[146],"points:":[148],"young,":[149],"middle-aged,":[150],"aged,":[152],"traditional":[156,191],"state-based":[157],"approach.":[164],"study":[167,186],"use":[169],"clustering":[171,177],"(SPICi)":[173],"designed":[174],"specifically":[175],"for":[176,206],"large":[179],"verify":[187],"an":[188,203],"inconsistency":[189],"identification":[195],"approaches":[196,214],"enrichment.":[199],"These":[200],"highlight":[202],"intriguing":[204],"issue":[205],"those":[207],"performing,":[208],"critiquing,":[209],"based":[213,232],"their":[216],"research":[217,233],"black":[221],"box":[222],"workflow":[224],"type":[225],"used":[229],"supplemented":[236],"transitionbased":[239],"support":[242],"movement":[243],"silico":[246],"vivo":[249],"experimentation":[250],"target":[252],"genes.":[253]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
