{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:24:24Z","timestamp":1762899864677,"version":"3.37.3"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T00:00:00Z","timestamp":1580083200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11931008","61801265","61877064","31571354","61771009"],"award-info":[{"award-number":["11931008","61801265","61877064","31571354","61771009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2018PA001"],"award-info":[{"award-number":["ZR2018PA001"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"KAUST","doi-asserted-by":"publisher","award":["FCC\/1\/1976-18-01","FCC\/1\/1976-23-01","FCC\/1\/1976-25-01","FCC\/1\/1976-26-01","FCS\/1\/4102-02-01","URF\/1\/4098-01-01"],"award-info":[{"award-number":["FCC\/1\/1976-18-01","FCC\/1\/1976-23-01","FCC\/1\/1976-25-01","FCC\/1\/1976-26-01","FCS\/1\/4102-02-01","URF\/1\/4098-01-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Full-length transcript reconstruction is very important and quite challenging for the widely used RNA-seq data analysis. Currently, available RNA-seq assemblers generally suffered from serious limitations in practical applications, such as low assembly accuracy and incompatibility with latest alignment tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce iPAC, a new genome-guided assembler for reconstruction of isoforms, which revolutionizes the usage of paired-end and sequencing depth information via phasing and combing paths over a newly designed phasing graph. Tested on both simulated and real datasets, it is to some extent superior to all the salient assemblers of the same kind. Especially, iPAC is significantly powerful in recovery of lowly expressed transcripts while others are not.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>iPAC is freely available at http:\/\/sourceforge.net\/projects\/transassembly\/files.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa052","type":"journal-article","created":{"date-parts":[[2020,1,20]],"date-time":"2020-01-20T20:10:46Z","timestamp":1579551046000},"page":"2712-2717","source":"Crossref","is-referenced-by-count":5,"title":["iPAC: a genome-guided assembler of isoforms via phasing and combing paths"],"prefix":"10.1093","volume":"36","author":[{"given":"Ting","family":"Yu","sequence":"first","affiliation":[{"name":"School of Mathematics , Shandong University, Jinan 250100, China"}]},{"given":"Juntao","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Mathematics , Shandong University, Jinan 250100, China"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Computer , Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia"}]},{"given":"Guojun","family":"Li","sequence":"additional","affiliation":[{"name":"School of Mathematics , Shandong University, Jinan 250100, China"},{"name":"Research Center for Mathematics and Interdisciplinary Sciences , Shandong University, Qingdao 266237, China"}]}],"member":"286","published-online":{"date-parts":[[2020,1,27]]},"reference":[{"key":"2023013110293383800_btaa052-B1","doi-asserted-by":"crossref","first-page":"4570","DOI":"10.1093\/nar\/gkq211","article-title":"Detection of splice junctions from paired-end RNA-seq data by SpliceMap","volume":"38","author":"Au","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023013110293383800_btaa052-B2","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1093\/bioinformatics\/btt442","article-title":"MITIE: simultaneous RNA-seq-based transcript identification and quantification in multiple samples","volume":"29","author":"Behr","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013110293383800_btaa052-B3","doi-asserted-by":"crossref","first-page":"2872","DOI":"10.1093\/bioinformatics\/btp367","article-title":"De novo transcriptome assembly with ABySS","volume":"25","author":"Birol","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013110293383800_btaa052-B4","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","article-title":"Mechanisms of alternative pre-messenger RNA splicing","volume":"72","author":"Black","year":"2003","journal-title":"Annu. 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