{"id":"https://openalex.org/W3004548325","doi":"https://doi.org/10.1109/bibm47256.2019.8983180","title":"RNA Transcript Assembly Using Inexact Flows","display_name":"RNA Transcript Assembly Using Inexact Flows","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004548325","doi":"https://doi.org/10.1109/bibm47256.2019.8983180","mag":"3004548325"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983180","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983180","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 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/A5023404314","display_name":"Lucia Williams","orcid":"https://orcid.org/0000-0003-3785-0247"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucia Williams","raw_affiliation_strings":["Gianforte School of Computing, Montana State University,Bozeman,USA","Gianforte School of Computing, Montana State University, Bozeman, USA"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University,Bozeman,USA","institution_ids":["https://openalex.org/I23732399"]},{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027506836","display_name":"Gillian Reynolds","orcid":"https://orcid.org/0000-0001-6233-6915"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gillian Reynolds","raw_affiliation_strings":["Gianforte School of Computing, Montana State University,Bozeman,USA","Gianforte School of Computing, Montana State University, Bozeman, USA"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University,Bozeman,USA","institution_ids":["https://openalex.org/I23732399"]},{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084888509","display_name":"Brendan Mumey","orcid":"https://orcid.org/0000-0001-7151-2124"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brendan Mumey","raw_affiliation_strings":["Gianforte School of Computing, Montana State University,Bozeman,USA","Gianforte School of Computing, Montana State University, Bozeman, USA"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University,Bozeman,USA","institution_ids":["https://openalex.org/I23732399"]},{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, USA","institution_ids":["https://openalex.org/I23732399"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023404314"],"corresponding_institution_ids":["https://openalex.org/I23732399"],"apc_list":null,"apc_paid":null,"fwci":0.4262,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.6287298,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1907","last_page":"1914"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9968000054359436,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9968000054359436,"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/T12072","display_name":"Machine Learning and Algorithms","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9868999719619751,"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":0.5739297866821289},{"id":"https://openalex.org/keywords/flow","display_name":"Flow (mathematics)","score":0.5719048380851746},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.5561964511871338},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.4786873459815979},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47314703464508057},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4677795171737671},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.4456942081451416},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3235844373703003},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26961302757263184},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19819417595863342},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09245681762695312}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5739297866821289},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.5719048380851746},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.5561964511871338},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.4786873459815979},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47314703464508057},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4677795171737671},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.4456942081451416},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3235844373703003},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26961302757263184},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19819417595863342},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09245681762695312},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983180","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983180","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":27,"referenced_works":["https://openalex.org/W1981509058","https://openalex.org/W1983426138","https://openalex.org/W2053057991","https://openalex.org/W2054576015","https://openalex.org/W2068289888","https://openalex.org/W2092467693","https://openalex.org/W2098809361","https://openalex.org/W2104005232","https://openalex.org/W2126766730","https://openalex.org/W2141458291","https://openalex.org/W2149342630","https://openalex.org/W2164946254","https://openalex.org/W2178294617","https://openalex.org/W2236822143","https://openalex.org/W2271526763","https://openalex.org/W2287064828","https://openalex.org/W2291157727","https://openalex.org/W2415680291","https://openalex.org/W2523787414","https://openalex.org/W2604182897","https://openalex.org/W2605455299","https://openalex.org/W2606548143","https://openalex.org/W2773298966","https://openalex.org/W2791864720","https://openalex.org/W2938447273","https://openalex.org/W2951951814","https://openalex.org/W2963833316"],"related_works":["https://openalex.org/W2392243736","https://openalex.org/W86652014","https://openalex.org/W2380059383","https://openalex.org/W4224278052","https://openalex.org/W2063679720","https://openalex.org/W2328518092","https://openalex.org/W3101249758","https://openalex.org/W2382079200","https://openalex.org/W3129895999","https://openalex.org/W2374091470"],"abstract_inverted_index":{"RNA-Seq":[0],"technology":[1],"allows":[2],"for":[3,67,154],"high-throughput,":[4],"low":[5],"cost":[6],"measurement":[7,96],"of":[8,20,47],"gene":[9],"expression.":[10],"An":[11],"important":[12],"step":[13],"in":[14,38,70,127,130,195],"this":[15,57,75,116,155],"process":[16],"is":[17,42,111,152,161,177],"the":[18,40,45,61,77,112,121,140,157,178,182,198],"assembly":[19],"mRNA":[21],"transcript":[22],"short":[23],"reads":[24],"into":[25],"full":[26],"transcripts.":[27],"The":[28,108],"problem":[29,37,81,117],"can":[30,202],"be":[31,203],"viewed":[32],"as":[33,76],"a":[34,53,134,149],"flow":[35,63,145,183],"decomposition":[36,146,184],"which":[39],"objective":[41],"to":[43,51,65,87,115,132,181],"minimize":[44],"number":[46],"path":[48],"flows":[49],"needed":[50],"represent":[52],"given":[54],"flow.":[55,135],"In":[56,90,136],"work":[58],"we":[59],"relax":[60],"edge":[62,126],"constraints":[64],"allow":[66],"some":[68],"uncertainty":[69],"their":[71],"measurement.":[72],"We":[73],"formulate":[74],"Inexact":[78],"Flow":[79],"Decomposition":[80],"and":[82,98],"propose":[83],"an":[84,137,143],"algorithmic":[85],"strategy":[86],"solve":[88],"it.":[89],"practice,":[91],"real":[92],"biological":[93,190],"data":[94,191],"has":[95],"errors":[97],"so":[99],"experimentally-derived":[100],"edge-weighted":[101],"splice":[102],"graphs":[103,129],"are":[104],"often":[105],"not":[106],"flows.":[107],"proposed":[109],"method":[110,141,151],"first":[113],"approach":[114],"that":[118,194],"explicitly":[119],"controls":[120],"error":[122],"allowed":[123],"on":[124,188],"each":[125],"these":[128],"order":[131],"achieve":[133],"intermediate":[138],"step,":[139,156],"solves":[142],"exact":[144],"instance;":[147],"if":[148],"greedy":[150],"used":[153],"overall":[158],"running":[159],"time":[160],"O(|E|":[162],"<sup":[163,167,171],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[164,168,172],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">2</sup>":[165,169],"|V|":[166],"+|P|":[170],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">3</sup>":[173],"),":[174],"where":[175],"P":[176],"solution":[179],"found":[180],"instance.":[185],"Preliminary":[186],"results":[187],"simulated":[189],"sets":[192],"show":[193],"many":[196],"cases":[197],"ground":[199],"truth":[200],"paths":[201],"recovered":[204],"at":[205],"approximately":[206],"correct":[207],"abundances,":[208],"even":[209],"with":[210],"noisy":[211],"input":[212],"data.":[213]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}