{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T13:45:53Z","timestamp":1778852753190,"version":"3.51.4"},"reference-count":118,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,4,19]],"date-time":"2021-04-19T00:00:00Z","timestamp":1618790400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Key Research and Development Project of China","award":["2019YFA0706202"],"award-info":[{"award-number":["2019YFA0706202"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61702054"],"award-info":[{"award-number":["61702054"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018579","name":"Training Program for Excellent Young Innovators of Changsha","doi-asserted-by":"crossref","award":["kq2009093"],"award-info":[{"award-number":["kq2009093"]}],"id":[{"id":"10.13039\/501100018579","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100018579","name":"Training Program for Excellent Young Innovators of Changsha","doi-asserted-by":"crossref","award":["kq1905045"],"award-info":[{"award-number":["kq1905045"]}],"id":[{"id":"10.13039\/501100018579","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundamental Research Funds for the Central Universities of Central South University","award":["2019zzts279"],"award-info":[{"award-number":["2019zzts279"]}]},{"name":"Degree & Postgraduate Education Reform Project of Hunan Province","award":["2019JGYB051"],"award-info":[{"award-number":["2019JGYB051"]}]},{"name":"Hunan Provincial Science and Technology Program","award":["2019CB1007"],"award-info":[{"award-number":["2019CB1007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The prediction of genes related to diseases is important to the study of the diseases due to high cost and time consumption of biological experiments. Network propagation is a popular strategy for disease-gene prediction. However, existing methods focus on the stable solution of dynamics while ignoring the useful information hidden in the dynamical process, and it is still a challenge to make use of multiple types of physical\/functional relationships between proteins\/genes to effectively predict disease-related genes. Therefore, we proposed a framework of network impulsive dynamics on multiplex biological network (NIDM) to predict disease-related genes, along with four variants of NIDM models and four kinds of impulsive dynamical signatures (IDSs). NIDM is to identify disease-related genes by mining the dynamical responses of nodes to impulsive signals being exerted at specific nodes. By a series of experimental evaluations in various types of biological networks, we confirmed the advantage of multiplex network and the important roles of functional associations in disease-gene prediction, demonstrated superior performance of NIDM compared with four types of network-based algorithms and then gave the effective recommendations of NIDM models and IDS signatures. To facilitate the prioritization and analysis of (candidate) genes associated to specific diseases, we developed a user-friendly web server, which provides three kinds of filtering patterns for genes, network visualization, enrichment analysis and a wealth of external links (http:\/\/bioinformatics.csu.edu.cn\/DGP\/NID.jsp). NIDM is a protocol for disease-gene prediction integrating different types of biological networks, which may become a very useful computational tool for the study of disease-related genes.<\/jats:p>","DOI":"10.1093\/bib\/bbab080","type":"journal-article","created":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T12:16:24Z","timestamp":1613996184000},"source":"Crossref","is-referenced-by-count":36,"title":["NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3045-5706","authenticated-orcid":false,"given":"Ju","family":"Xiang","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, Human, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiashuai","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, Human, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruiqing","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingyi","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0188-1394","authenticated-orcid":false,"given":"Min","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, Changsha, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,4,19]]},"reference":[{"key":"2021090817433204600_ref1","doi-asserted-by":"crossref","first-page":"2345","DOI":"10.1126\/science.1076641","article-title":"Finding genes that underlie complex traits","volume":"298","author":"Glazier","year":"2002","journal-title":"Science"},{"key":"2021090817433204600_ref2","doi-asserted-by":"crossref","first-page":"294","DOI":"10.3389\/fgene.2019.00294","article-title":"Network medicine in the age of biomedical big data","volume":"10","author":"Sonawane","year":"2019","journal-title":"Front Genet"},{"key":"2021090817433204600_ref3","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/ng1090","article-title":"Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease","volume":"33","author":"Botstein","year":"2003","journal-title":"Nat 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