{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:33:53Z","timestamp":1778632433495,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,2,2]],"date-time":"2018-02-02T00:00:00Z","timestamp":1517529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"National Natural Science Foundation for Young Scientists of China","award":["31501070"],"award-info":[{"award-number":["31501070"]}]},{"DOI":"10.13039\/501100004607","name":"Natural Science Foundation of Guangxi Province","doi-asserted-by":"publisher","award":["2016GXNSFCA380006"],"award-info":[{"award-number":["2016GXNSFCA380006"]}],"id":[{"id":"10.13039\/501100004607","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Hubei Province, China","award":["2017CFB137"],"award-info":[{"award-number":["2017CFB137"]}]},{"name":"Scientific Research Foundation of GuangXi University","award":["XGZ150316"],"award-info":[{"award-number":["XGZ150316"]}]},{"name":"Australian Research Council Discovery","award":["130102124"],"award-info":[{"award-number":["130102124"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Antigens that contain overlapping epitopes have been occasionally reported. As current algorithms mainly take a one-antigen-one-epitope approach to the prediction of epitopes, they are not capable of detecting these multiple and overlapping epitopes accurately, or even those multiple and separated epitopes existing in some other antigens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce a novel subgraph clustering algorithm for more accurate detection of epitopes. This algorithm takes graph partitions as seeds, and expands the seeds to merge overlapping subgraphs based on the term frequency-inverse document frequency (TF-IDF) featured similarity. Then, the merged subgraphs are each classified as an epitope or non-epitope. Tests of our algorithm were conducted on three newly collected datasets of antigens. In the first dataset, each antigen contains only a single epitope; in the second, each antigen contains only multiple and separated epitopes; and in the third, each antigen contains overlapping epitopes. The prediction performance of our algorithm is significantly better than the state-of-art methods. The lifts of the averaged f-scores on top of the best existing methods are 60, 75 and 22% for the single epitope detection, the multiple and separated epitopes detection, and the overlapping epitopes detection, respectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code is available at github.com\/lzhlab\/glep\/.<\/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\/bty051","type":"journal-article","created":{"date-parts":[[2018,2,1]],"date-time":"2018-02-01T20:11:44Z","timestamp":1517515904000},"page":"2061-2068","source":"Crossref","is-referenced-by-count":6,"title":["Novel overlapping subgraph clustering for the detection of antigen epitopes"],"prefix":"10.1093","volume":"34","author":[{"given":"Liang","family":"Zhao","sequence":"first","affiliation":[{"name":"Department of Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Hubei, China"},{"name":"Department of Computer Science, School of Computing and Electronic Information, Guangxi University, Nanning, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaogui","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, School of Computing and Electronic Information, Guangxi University, Nanning, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiawen","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wencui","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1833-7413","authenticated-orcid":false,"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Data Science, Advanced Analytics Institute, Faculty of Engineering and IT, University of Technology Sydney, Broadway, NSW 2007, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,2,2]]},"reference":[{"key":"2023012713380554000_bty051-B1","volume-title":"Cellular and Molecular Immunology","author":"Abbas","year":"2009","edition":"6th edn."},{"key":"2023012713380554000_bty051-B2","doi-asserted-by":"crossref","first-page":"e0169535","DOI":"10.1371\/journal.pone.0169535","article-title":"Antibodies targeting closely adjacent or minimally overlapping epitopes can displace one another","volume":"12","author":"Abdiche","year":"2017","journal-title":"Plos One"},{"key":"2023012713380554000_bty051-B3","first-page":"105","volume-title":"Overlapping Community Discovery Methods: A Survey","author":"Amelio","year":"2014"},{"key":"2023012713380554000_bty051-B4","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell\u2019s functional organization","volume":"5","author":"Barabasi","year":"2004","journal-title":"Nat. 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