{"id":"https://openalex.org/W2345129658","doi":"https://doi.org/10.5220/0005819702720277","title":"On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy","display_name":"On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2345129658","doi":"https://doi.org/10.5220/0005819702720277","mag":"2345129658"},"language":"en","primary_location":{"id":"doi:10.5220/0005819702720277","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0005819702720277","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0005819702720277","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011459984","display_name":"Anna Kuosmanen","orcid":"https://orcid.org/0000-0002-7002-0803"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Anna Kuosmanen","raw_affiliation_strings":["University of Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046627176","display_name":"Ahmed Sobih","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ahmed Sobih","raw_affiliation_strings":["University of Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061874157","display_name":"Rom\u00e9o Rizzi","orcid":"https://orcid.org/0000-0002-2387-0952"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Romeo Rizzi","raw_affiliation_strings":["University of Verona, Italy"],"affiliations":[{"raw_affiliation_string":"University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veli M\u00e4kinen","raw_affiliation_strings":["University of Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063897224","display_name":"Alexandru I. Tomescu","orcid":"https://orcid.org/0000-0002-5747-8350"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Alexandru I. Tomescu","raw_affiliation_strings":["University of Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011459984"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":null,"apc_paid":null,"fwci":0.8336,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.75091069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"272","last_page":"277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983000159263611,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9973999857902527,"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":0.6716512441635132},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5992833971977234},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5237013101577759},{"id":"https://openalex.org/keywords/cover","display_name":"Cover (algebra)","score":0.4739815294742584},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4484538733959198},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4212009608745575},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.41439980268478394},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4060210883617401},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3649716079235077},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3257400393486023},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1663404107093811},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15210023522377014},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.14385885000228882},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13133296370506287},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09083333611488342}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6716512441635132},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5992833971977234},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5237013101577759},{"id":"https://openalex.org/C2780428219","wikidata":"https://www.wikidata.org/wiki/Q16952335","display_name":"Cover (algebra)","level":2,"score":0.4739815294742584},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4484538733959198},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4212009608745575},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.41439980268478394},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4060210883617401},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3649716079235077},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3257400393486023},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1663404107093811},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15210023522377014},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.14385885000228882},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13133296370506287},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09083333611488342},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5220/0005819702720277","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0005819702720277","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.5220/0005819702720277","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0005819702720277","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1975963573","https://openalex.org/W1999574084","https://openalex.org/W2000875411","https://openalex.org/W2048120844","https://openalex.org/W2053057991","https://openalex.org/W2057052228","https://openalex.org/W2088844778","https://openalex.org/W2097860373","https://openalex.org/W2102619694","https://openalex.org/W2104005232","https://openalex.org/W2106678197","https://openalex.org/W2112232553","https://openalex.org/W2114104545","https://openalex.org/W2126766730","https://openalex.org/W2141458291","https://openalex.org/W2143447881","https://openalex.org/W2149238618","https://openalex.org/W2151450179","https://openalex.org/W2152239989","https://openalex.org/W2155839887","https://openalex.org/W2208431757","https://openalex.org/W2231769377","https://openalex.org/W2248731764","https://openalex.org/W2558692177"],"related_works":["https://openalex.org/W2075768550","https://openalex.org/W3022218857","https://openalex.org/W2369178846","https://openalex.org/W2082716031","https://openalex.org/W2370289839","https://openalex.org/W4232403550","https://openalex.org/W623607250","https://openalex.org/W2933494595","https://openalex.org/W4313347705","https://openalex.org/W2070875930"],"abstract_inverted_index":{"Over":[0],"the":[1,34,71,78,81,100,143,151,162,171],"past":[2],"decade,":[3],"sequencing":[4,157],"read":[5,180],"length":[6],"has":[7],"increased":[8],"from":[9,26],"tens":[10],"to":[11,15,30,63,80,126],"hundreds":[12],"and":[13,106,137,148,158],"then":[14],"thousands":[16],"of":[17,47,99,119,176],"bases.":[18],"Current":[19],"cDNA":[20],"synthesis":[21],"methods":[22],"prevent":[23],"RNA-seq":[24],"reads":[25,39,129],"being":[27],"long":[28,38,128,183],"enough":[29],"entirely":[31],"capture":[32],"all":[33],"RNA":[35],"transcripts,":[36],"but":[37],"can":[40],"still":[41],"provide":[42],"connectivity":[43,60],"information":[44,61],"on":[45],"chains":[46],"multiple":[48],"exons":[49],"that":[50,57],"are":[51],"included":[52],"in":[53,90,140,150],"transcripts.":[54],"We":[55,113],"demonstrate":[56],"exploiting":[58],"full":[59],"leads":[62],"significantly":[64],"higher":[65],"prediction":[66],"accuracy,":[67],"as":[68],"measured":[69],"by":[70,110,156],"F-score.":[72],"For":[73],"this":[74,141],"purpose":[75],"we":[76],"implemented":[77],"solution":[79],"Minimum":[82,102],"Path":[83,103],"Cover":[84,104],"with":[85],"Subpath":[86],"Constraints":[87],"problem":[88,105,144,163],"introduced":[89,155],"(Rizzi":[91],"et":[92],"al.,":[93],"2014),":[94],"which":[95],"is":[96,124,145,188],"an":[97],"extension":[98],"classical":[101],"was":[107],"shown":[108],"solvable":[109],"min-cost":[111],"flows.":[112],"show":[114],"that,":[115],"under":[116],"hypothetical":[117],"conditions":[118],"perfect":[120],"sequencing,":[121],"our":[122,167],"approach":[123],"able":[125],"use":[127],"more":[130],"effectively":[131],"than":[132],"two":[133],"state-of-the-art":[134],"tools,":[135],"StringTie":[136],"FlipFlop.":[138],"Even":[139],"setting":[142],"not":[146],"trivial,":[147],"errors":[149,160],"underlying":[152],"flow":[153],"graph":[154],"alignment":[159],"complicate":[161],"further.":[164],"As":[165],"such":[166],"work":[168],"also":[169],"demonstrates":[170],"need":[172],"for":[173,182],"a":[174,177],"development":[175],"good":[178],"spliced":[179],"aligner":[181],"reads.":[184],"Our":[185],"proof-of-concept":[186],"implementation":[187],"available":[189],"at":[190],"http://www.cs.helsinki.fi/en/gsa/traphlor.":[191]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2016,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}