{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T19:01:10Z","timestamp":1777748470335,"version":"3.51.4"},"reference-count":0,"publisher":"SAGE Publications","issue":"5-6","license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation"],"published-print":{"date-parts":[[2012,11]]},"abstract":"<jats:p>\n                    The paper addresses the problem of how to use RNA-Seq data for transcriptome\n          reconstruction and quantification, as well as novel transcript discovery in partially\n          annotated genomes. We present a novel annotation-guided general framework for\n          transcriptome discovery, reconstruction and quantification in partially annotated genomes\n          and compare it with existing annotation-guided and genome-guided transcriptome assembly\n          methods. Our method, referred as\n                    <jats:bold>D<\/jats:bold>\n                    iscovery and\n                    <jats:bold>R<\/jats:bold>\n                    econstruction of\n                    <jats:bold>U<\/jats:bold>\n                    nannotated\n                    <jats:bold>T<\/jats:bold>\n                    ranscripts (DRUT), can be used to enhance\n          existing transcriptome assemblers, such as Cufflinks [3], as well as to accurately\n          estimate the transcript frequencies. Empirical analysis on synthetic datasets confirms\n          that Cufflinks enhanced by DRUT has superior quality of reconstruction and frequency\n          estimation of transcripts.\n                  <\/jats:p>","DOI":"10.3233\/isb-2012-0459","type":"journal-article","created":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T06:05:27Z","timestamp":1737353127000},"page":"251-261","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":2,"title":["Improved transcriptome quantification and reconstruction from RNA-Seq reads          using partial annotations"],"prefix":"10.1177","volume":"11","author":[{"given":"Serghei","family":"Mangul","sequence":"first","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian","family":"Caciula","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga","family":"Glebova","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ion","family":"Mandoiu","sequence":"additional","affiliation":[{"name":"Department of Computer Science &amp; Engineering, University of Connecticut,\r          Storrs, CT, USA, E-mail: ion@engr.uconn.edu"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Zelikovsky","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2012,1]]},"container-title":["In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/ISB-2012-0459","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/ISB-2012-0459","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T11:49:21Z","timestamp":1777463361000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.3233\/ISB-2012-0459"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1]]},"references-count":0,"journal-issue":{"issue":"5-6","published-print":{"date-parts":[[2012,11]]}},"alternative-id":["10.3233\/ISB-2012-0459"],"URL":"https:\/\/doi.org\/10.3233\/isb-2012-0459","relation":{},"ISSN":["1386-6338","1434-3207"],"issn-type":[{"value":"1386-6338","type":"print"},{"value":"1434-3207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,1]]}}}