{"id":"https://openalex.org/W2030646320","doi":"https://doi.org/10.1145/2382936.2382983","title":"An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads","display_name":"An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2030646320","doi":"https://doi.org/10.1145/2382936.2382983","mag":"2030646320"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2382983","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382983","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/A5017101305","display_name":"Serghei Mangul","orcid":"https://orcid.org/0000-0003-4770-3443"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Serghei Mangul","raw_affiliation_strings":["Georgia State University, Atlanta, GA","Georgia State University , Atlanta , GA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Georgia State University, Atlanta, GA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Georgia State University , Atlanta , GA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009449784","display_name":"Adrian Caciula","orcid":null},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrian Caciula","raw_affiliation_strings":["Georgia State University, Atlanta, GA","Georgia State University , Atlanta , GA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Georgia State University, Atlanta, GA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Georgia State University , Atlanta , GA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084402022","display_name":"Sahar Al Seesi","orcid":"https://orcid.org/0000-0002-7918-4791"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sahar Al Seesi","raw_affiliation_strings":["University of Connecticut, Storrs, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056793831","display_name":"Dumitru Brinza","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100234","display_name":"Life Systems (United States)","ror":"https://ror.org/010d6p438","country_code":"US","type":"company","lineage":["https://openalex.org/I4210100234"]},{"id":"https://openalex.org/I892709138","display_name":"Thermo Fisher Scientific (Norway)","ror":"https://ror.org/03x0ke992","country_code":"NO","type":"company","lineage":["https://openalex.org/I4210142480","https://openalex.org/I892709138"]}],"countries":["NO","US"],"is_corresponding":false,"raw_author_name":"Dumitru Brinza","raw_affiliation_strings":["Ion Bioinformatics, Life Technologies Corporation, Foster City, CA","Ion Bioinformatics, Life Technologies Corporation, Foster City, CA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ion Bioinformatics, Life Technologies Corporation, Foster City, CA","institution_ids":["https://openalex.org/I4210100234"]},{"raw_affiliation_string":"Ion Bioinformatics, Life Technologies Corporation, Foster City, CA#TAB#","institution_ids":["https://openalex.org/I892709138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078741197","display_name":"Abdul Rouf Banday","orcid":"https://orcid.org/0000-0002-1521-340X"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abdul Rouf Banday","raw_affiliation_strings":["University of Connecticut, Storrs, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066531693","display_name":"Rahul Kanadia","orcid":"https://orcid.org/0000-0001-7197-912X"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahul Kanadia","raw_affiliation_strings":["University of Connecticut, Storrs, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.4782,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.81088449,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"369","last_page":"376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9958000183105469,"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/computer-science","display_name":"Computer science","score":0.604912281036377},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5737922191619873},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5679934620857239},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.5103639960289001},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.4843614995479584},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.45246952772140503},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4446467161178589},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.42636218667030334},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38287127017974854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37040019035339355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2808889150619507},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25696051120758057},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1283969283103943}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.604912281036377},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5737922191619873},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5679934620857239},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.5103639960289001},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.4843614995479584},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.45246952772140503},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4446467161178589},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.42636218667030334},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38287127017974854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37040019035339355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2808889150619507},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25696051120758057},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1283969283103943}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2382936.2382983","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382983","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W162544871","https://openalex.org/W1493192698","https://openalex.org/W1988929438","https://openalex.org/W1989729446","https://openalex.org/W2000875411","https://openalex.org/W2011753019","https://openalex.org/W2034355012","https://openalex.org/W2037809979","https://openalex.org/W2038230536","https://openalex.org/W2055770801","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2098832713","https://openalex.org/W2107564978","https://openalex.org/W2112888168","https://openalex.org/W2118834857","https://openalex.org/W2122789575","https://openalex.org/W2126419817","https://openalex.org/W2141458291","https://openalex.org/W2150901760","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W2248731764"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W1021674602","https://openalex.org/W4362485661"],"abstract_inverted_index":{"Massively":[0],"parallel":[1],"whole":[2],"transcriptome":[3],"sequencing,":[4],"commonly":[5],"referred":[6],"to":[7,33,87],"as":[8,98],"RNA-Seq,":[9],"has":[10],"become":[11],"the":[12,34,105,116],"technology":[13],"of":[14,23,92,107],"choice":[15],"for":[16],"performing":[17],"gene":[18],"expression":[19],"profiling.":[20],"However,":[21],"reconstruction":[22,66],"full-length":[24],"novel":[25,47,64],"transcripts":[26,95,109],"from":[27,67],"RNA-Seq":[28,69,79],"data":[29],"remains":[30],"challenging":[31],"due":[32],"short":[35],"read":[36,131],"length":[37,61,118,151],"delivered":[38],"by":[39,129],"most":[40],"existing":[41],"sequencing":[42],"technologies.":[43],"We":[44],"propose":[45],"a":[46,73,111],"statistical":[48,113],"genome-guided":[49],"method":[50],"called":[51],"\"Transcriptome":[52],"Reconstruction":[53],"using":[54],"Integer":[55],"Programming\"":[56],"(TRIP)":[57],"that":[58,142],"incorporates":[59],"fragment":[60,117,126,150],"distribution":[62,119,152],"into":[63],"transcript":[65],"paired-end":[68],"reads.":[70],"TRIP":[71,143],"creates":[72],"splice":[74],"graph":[75],"based":[76],"on":[77,135],"aligned":[78],"reads":[80],"and":[81,125,138],"enumerates":[82],"all":[83],"maximal":[84],"paths":[85],"corresponding":[86],"putative":[88],"transcripts.":[89],"The":[90,154],"problem":[91],"selecting":[93],"true":[94],"is":[96,144,156],"formulated":[97],"an":[99],"integer":[100],"program":[101],"(IP)":[102],"which":[103],"minimizes":[104],"set":[106],"selected":[108],"yielding":[110],"good":[112],"fit":[114],"between":[115],"(empirically":[120],"determined":[121],"during":[122],"library":[123],"preparation)":[124],"lengths":[127],"implied":[128],"mapped":[130],"pairs.":[132],"Experimental":[133],"results":[134],"both":[136],"real":[137],"synthetic":[139],"datasets":[140],"show":[141],"more":[145],"accurate":[146],"than":[147],"methods":[148],"ignoring":[149],"information.":[153],"software":[155],"available":[157],"at:":[158],"http://www.cs.gsu.edu/serghei/?q=trip":[159]},"counts_by_year":[{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}