{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T19:51:30Z","timestamp":1777751490293,"version":"3.51.4"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,6,28]],"date-time":"2019-06-28T00:00:00Z","timestamp":1561680000000},"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":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61872300"],"award-info":[{"award-number":["61872300"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61873214"],"award-info":[{"award-number":["61873214"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871020"],"award-info":[{"award-number":["61871020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61571163"],"award-info":[{"award-number":["61571163"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61532014"],"award-info":[{"award-number":["61532014"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["XDJK2019B024"],"award-info":[{"award-number":["XDJK2019B024"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Research and Development Plan Task of China","award":["2016YFC0901902"],"award-info":[{"award-number":["2016YFC0901902"]}]},{"name":"Natural Science Foundation of CQ CSTC","award":["cstc2018jcyjAX0228"],"award-info":[{"award-number":["cstc2018jcyjAX0228"]}]},{"name":"Natural Science Foundation of CQ CSTC","award":["cstc2016jcyjA0351"],"award-info":[{"award-number":["cstc2016jcyjA0351"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Alternative splicing contributes to the functional diversity of protein species and the proteoforms translated from alternatively spliced isoforms of a gene actually execute the biological functions. Computationally predicting the functions of genes has been studied for decades. However, how to distinguish the functional annotations of isoforms, whose annotations are essential for understanding developmental abnormalities and cancers, is rarely explored. The main bottleneck is that functional annotations of isoforms are generally unavailable and functional genomic databases universally store the functional annotations at the gene level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose IsoFun to accomplish Isoform Function prediction based on bi-random walks on a heterogeneous network. IsoFun firstly constructs an isoform functional association network based on the expression profiles of isoforms derived from multiple RNA-seq datasets. Next, IsoFun uses the available Gene Ontology annotations of genes, gene\u2013gene interactions and the relations between genes and isoforms to construct a heterogeneous network. After this, IsoFun performs a tailored bi-random walk on the heterogeneous network to predict the association between GO terms and isoforms, thus accomplishing the prediction of GO annotations of isoforms. Experimental results show that IsoFun significantly outperforms the state-of-the-art algorithms and improves the area under the receiver-operating curve (AUROC) and the area under the precision-recall curve (AUPRC) by 17% and 44% at the gene-level, respectively. We further validated the performance of IsoFun on the genes ADAM15 and BCL2L1. IsoFun accurately differentiates the functions of respective isoforms of these two genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code of IsoFun is available at http:\/\/mlda.swu.edu.cn\/codes.php? name=IsoFun.<\/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\/btz535","type":"journal-article","created":{"date-parts":[[2019,6,26]],"date-time":"2019-06-26T11:18:25Z","timestamp":1561547905000},"page":"303-310","source":"Crossref","is-referenced-by-count":30,"title":["Isoform function prediction based on bi-random walks on a heterogeneous network"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1667-6705","authenticated-orcid":false,"given":"Guoxian","family":"Yu","sequence":"first","affiliation":[{"name":"College of Computer and Information Science, Southwest University , Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keyao","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science, Southwest University , Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlotta","family":"Domeniconi","sequence":"additional","affiliation":[{"name":"Department of Computer Science, George Mason University , Fairfax, VA 22030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maozu","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , Beijing, China"},{"name":"Beijing Key Laboratory of Intelligent Processing for Building Big Data, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5890-0365","authenticated-orcid":false,"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Computer and Information Science, Southwest University , Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,28]]},"reference":[{"key":"2023013109505474900_btz535-B1","first-page":"577","article-title":"Support vector machines for multiple-instance learning","author":"Andrews","year":"2003","journal-title":"Adv. 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