{"id":"https://openalex.org/W1996343102","doi":"https://doi.org/10.1145/2506583.2506589","title":"An Island-Based Approach for Differential Expression Analysis","display_name":"An Island-Based Approach for Differential Expression Analysis","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W1996343102","doi":"https://doi.org/10.1145/2506583.2506589","mag":"1996343102","pmid":"https://pubmed.ncbi.nlm.nih.gov/25632406"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506589","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506589","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4306332","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049771425","display_name":"Abdallah M. Eteleeb","orcid":"https://orcid.org/0000-0001-9045-250X"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Abdallah M. Eteleeb","raw_affiliation_strings":["Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA","Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]},{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, USA#TAB#","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062202807","display_name":"Robert M Flight","orcid":"https://orcid.org/0000-0001-8141-7788"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert M. Flight","raw_affiliation_strings":["Department of Chemistry, University of Louisville, Louisville, KY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060935645","display_name":"Benjamin J. Harrison","orcid":"https://orcid.org/0000-0002-6078-5060"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin J. Harrison","raw_affiliation_strings":["Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038602012","display_name":"Jeffrey C. Petruska","orcid":"https://orcid.org/0000-0002-3068-2677"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey C. Petruska","raw_affiliation_strings":["Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034707578","display_name":"Eric C. Rouchka","orcid":"https://orcid.org/0000-0003-3487-6572"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric C. Rouchka","raw_affiliation_strings":["Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA","Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]},{"raw_affiliation_string":"Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, USA#TAB#","institution_ids":["https://openalex.org/I142740786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049771425"],"corresponding_institution_ids":["https://openalex.org/I142740786"],"apc_list":null,"apc_paid":null,"fwci":0.4487,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64886107,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"2013","issue":null,"first_page":"419","last_page":"429"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9986000061035156,"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/rna-seq","display_name":"RNA-Seq","score":0.6943696737289429},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6091877222061157},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.49524179100990295},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4691392779350281},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.4481123387813568},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4415803551673889},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43678298592567444},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4291679263114929},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.4227150082588196},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.41682541370391846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40706175565719604},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.35832828283309937},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30592793226242065},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2605057954788208}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6943696737289429},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6091877222061157},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.49524179100990295},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4691392779350281},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.4481123387813568},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4415803551673889},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43678298592567444},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4291679263114929},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.4227150082588196},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.41682541370391846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40706175565719604},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.35832828283309937},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30592793226242065},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2605057954788208},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/2506583.2506589","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506589","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},{"id":"pmid:25632406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25632406","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":"2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics : ACM - BCB 2013 : Washington, D.C., U.S.A., September 22 - 25, 2013. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informa...","raw_type":null},{"id":"pmh:oai:europepmc.org:3272128","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC4306332","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4306332","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4306332","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM Conf Bioinform Comput Biol Biomed Inform (2013)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4306332","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4306332","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM Conf Bioinform Comput Biol Biomed Inform (2013)","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","score":0.8700000047683716,"display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309490","display_name":"Paralyzed Veterans of America","ror":"https://ror.org/00pfg3v73"},{"id":"https://openalex.org/F4320313699","display_name":"Kentucky Spinal Cord and Head Injury Research Trust","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W179094737","https://openalex.org/W1489054197","https://openalex.org/W1533179050","https://openalex.org/W1544691147","https://openalex.org/W1615688534","https://openalex.org/W1969369730","https://openalex.org/W1974451383","https://openalex.org/W1981509058","https://openalex.org/W1989367702","https://openalex.org/W2010637767","https://openalex.org/W2023978699","https://openalex.org/W2027455260","https://openalex.org/W2034355012","https://openalex.org/W2061537056","https://openalex.org/W2063370830","https://openalex.org/W2070064901","https://openalex.org/W2096465161","https://openalex.org/W2101989368","https://openalex.org/W2102619694","https://openalex.org/W2110065044","https://openalex.org/W2112888168","https://openalex.org/W2114104545","https://openalex.org/W2114405789","https://openalex.org/W2119034410","https://openalex.org/W2121211805","https://openalex.org/W2124985265","https://openalex.org/W2126419817","https://openalex.org/W2130395351","https://openalex.org/W2141458291","https://openalex.org/W2142023052","https://openalex.org/W2146648681","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2156841387","https://openalex.org/W2159479647","https://openalex.org/W2169674658","https://openalex.org/W6631984995"],"related_works":["https://openalex.org/W2068174058","https://openalex.org/W2800537687","https://openalex.org/W2147652847","https://openalex.org/W1976843764","https://openalex.org/W3215633333","https://openalex.org/W2001319824","https://openalex.org/W2067501355","https://openalex.org/W2349910028","https://openalex.org/W1671586832","https://openalex.org/W2163313682"],"abstract_inverted_index":{"High-throughput":[0],"mRNA":[1],"sequencing":[2,116],"(also":[3],"known":[4,81],"as":[5,208],"RNA-Seq)":[6],"promises":[7],"to":[8,23,61,80,146,153,180],"be":[9,94,141],"the":[10,21,44,51,69,75,158,172,181],"technique":[11,19],"of":[12,43,46,71,77,123,132,160,174],"choice":[13],"for":[14,27,108],"studying":[15],"transcriptome":[16],"profiles.":[17],"This":[18,67],"provides":[20],"ability":[22],"develop":[24],"precise":[25],"methodologies":[26],"transcript":[28,34],"and":[29,35,38,74,114,170,190],"gene":[30,185],"expression":[31,63,72,111,133],"quantification,":[32],"novel":[33,103],"exon":[36],"discovery,":[37],"splice":[39],"variant":[40],"detection.":[41],"One":[42],"limitations":[45],"current":[47],"RNA-Seq":[48,113,196],"methods":[49,204],"is":[50],"dependency":[52],"on":[53,135],"annotated":[54],"biological":[55],"features":[56],"(e.g.":[57],"exons,":[58],"transcripts,":[59],"genes)":[60],"detect":[62,154],"differences":[64],"across":[65,143],"samples.":[66],"forces":[68],"identification":[70],"levels":[73],"detection":[76],"significant":[78,85],"changes":[79,86],"genomic":[82],"regions.":[83],"Any":[84],"that":[87,139],"occur":[88],"in":[89,112,205],"unannotated":[90],"regions":[91],"will":[92],"not":[93],"captured.":[95],"To":[96],"overcome":[97],"this":[98],"limitation,":[99],"we":[100],"developed":[101],"a":[102],"segmentation":[104,128],"approach,":[105],"Island-Based":[106],"(IB),":[107],"analyzing":[109],"differential":[110,148],"targeted":[115],"(exome":[117],"capture)":[118],"data":[119],"without":[120],"specific":[121],"knowledge":[122],"an":[124,211],"isoform.":[125],"The":[126,198],"IB":[127,199],"determines":[129],"individual":[130],"islands":[131,161],"based":[134],"windowed":[136],"read":[137],"counts":[138],"can":[140],"compared":[142],"experimental":[144],"conditions":[145],"determine":[147],"island":[149],"expression.":[150],"In":[151],"order":[152],"differentially":[155,183],"expressed":[156,184],"genes,":[157],"significance":[159],"(p-values)":[162],"are":[163],"combined":[164],"using":[165,192],"Fisher's":[166],"method.":[167],"We":[168],"tested":[169],"evaluated":[171],"performance":[173],"our":[175],"approach":[176],"by":[177,210],"comparing":[178],"it":[179],"existing":[182],"(DEG)":[186],"methods:":[187],"CuffDiff,":[188],"DESeq,":[189],"edgeR":[191],"two":[193],"benchmark":[194],"MAQC":[195],"datasets.":[197],"algorithm":[200],"outperforms":[201],"all":[202],"three":[203],"both":[206],"datasets":[207],"illustrated":[209],"increased":[212],"auROC.":[213]},"counts_by_year":[{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}