{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T19:03:27Z","timestamp":1742929407556,"version":"3.40.3"},"publisher-location":"Cham","reference-count":38,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030202415"},{"type":"electronic","value":"9783030202422"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-20242-2_11","type":"book-chapter","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T14:34:37Z","timestamp":1558362877000},"page":"127-137","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Identifying Human Essential Genes by Network Embedding Protein-Protein Interaction Network"],"prefix":"10.1007","author":[{"given":"Wei","family":"Dai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiancheng","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongjiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,5,9]]},"reference":[{"issue":"Database issue","key":"11_CR1","doi-asserted-by":"publisher","first-page":"D455","DOI":"10.1093\/nar\/gkn858","volume":"37","author":"R Zhang","year":"2009","unstructured":"Zhang, R., Lin, Y.: DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37(Database issue), D455\u2013D458 (2009)","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"11_CR2","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1038\/nchembio.2007.24","volume":"3","author":"AE Clatworthy","year":"2007","unstructured":"Clatworthy, A.E., Pierson, E., Hung, D.T.: Targeting virulence: a new paradigm for antimicrobial therapy. Nat. Chem. Biol. 3(9), 541\u2013548 (2007)","journal-title":"Nat. Chem. Biol."},{"issue":"1","key":"11_CR3","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1186\/1471-2164-7-165","volume":"7","author":"S Furney","year":"2006","unstructured":"Furney, S., Alba, M.M., Lopez-Bigas, N.: Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genom. 7(1), 165 (2006)","journal-title":"BMC Genom."},{"key":"11_CR4","doi-asserted-by":"publisher","first-page":"6869","DOI":"10.1038\/nature00935","volume":"418","author":"G Giaever","year":"2002","unstructured":"Giaever, G., et al.: Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 6869 (2002)","journal-title":"Nature"},{"issue":"1","key":"11_CR5","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1046\/j.1365-2958.2003.03697.x","volume":"50","author":"TJB Roemer","year":"2010","unstructured":"Roemer, T.J.B., et al.: Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol. Microbiol. 50(1), 167\u2013181 (2010)","journal-title":"Mol. Microbiol."},{"issue":"3","key":"11_CR6","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1111\/j.1440-1711.2005.01332.x","volume":"83","author":"LM Cullen","year":"2005","unstructured":"Cullen, L.M., Arndt, G.M.: Genome-wide screening for gene function using RNAi in mammalian cells. Immunol. Cell Biol. 83(3), 217\u2013223 (2005)","journal-title":"Immunol. Cell Biol."},{"issue":"6","key":"11_CR7","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.cels.2015.12.007","volume":"1","author":"A Fraser","year":"2015","unstructured":"Fraser, A.: Essential human genes. Cell Syst. 1(6), 381\u2013382 (2015)","journal-title":"Cell Syst."},{"issue":"6","key":"11_CR8","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1016\/j.cell.2015.11.015","volume":"163","author":"T Hart","year":"2015","unstructured":"Hart, T., et al.: High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 163(6), 1515\u20131526 (2015)","journal-title":"Cell"},{"issue":"6264","key":"11_CR9","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1126\/science.aac7041","volume":"350","author":"T Wang","year":"2015","unstructured":"Wang, T., et al.: Identification and characterization of essential genes in the human genome. Science 350(6264), 1096\u20131101 (2015)","journal-title":"Science"},{"issue":"5","key":"11_CR10","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/bioinformatics\/bti058","volume":"21","author":"Y Chen","year":"2005","unstructured":"Chen, Y., Xu, D.: Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics 21(5), 575\u2013581 (2005)","journal-title":"Bioinformatics"},{"issue":"9","key":"11_CR11","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1093\/bioinformatics\/bts120","volume":"28","author":"Y Yuan","year":"2012","unstructured":"Yuan, Y., et al.: Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data. Bioinformatics 28(9), 1246\u20131252 (2012)","journal-title":"Bioinformatics"},{"issue":"8","key":"11_CR12","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.1105\/tpc.15.00051","volume":"27","author":"JP Lloyd","year":"2015","unstructured":"Lloyd, J.P., et al.: Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes. Plant Cell 27(8), 2133 (2015)","journal-title":"Plant Cell"},{"issue":"1\u20132","key":"11_CR13","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1002\/prca.201200068","volume":"7","author":"J Wang","year":"2013","unstructured":"Wang, J., Peng, W., Wu, F.X.: Computational approaches to predicting essential proteins: a survey. PROTEOMICS-Clin. Appl. 7(1\u20132), 181\u2013192 (2013)","journal-title":"PROTEOMICS-Clin. Appl."},{"issue":"6833","key":"11_CR14","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong, H., et al.: Lethality and centrality in protein networks. Nature 411(6833), 41\u201342 (2001)","journal-title":"Nature"},{"issue":"2","key":"11_CR15","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1155\/JBB.2005.96","volume":"2005","author":"MP Joy","year":"2005","unstructured":"Joy, M.P., et al.: High-betweenness proteins in the yeast protein interaction network. J. Biomed. Biotechnol. 2005(2), 96\u2013103 (2005)","journal-title":"J. Biomed. Biotechnol."},{"issue":"1","key":"11_CR16","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0022-5193(03)00071-7","volume":"223","author":"S Wuchty","year":"2003","unstructured":"Wuchty, S., Stadler, P.F.: Centers of complex networks. J. Theor. Biol. 223(1), 45\u201353 (2003)","journal-title":"J. Theor. Biol."},{"issue":"4","key":"11_CR17","doi-asserted-by":"publisher","first-page":"e5344","DOI":"10.1371\/journal.pone.0005344","volume":"4","author":"RR Vallabhajosyula","year":"2009","unstructured":"Vallabhajosyula, R.R., et al.: Identifying hubs in protein interaction networks. PLoS ONE 4(4), e5344 (2009)","journal-title":"PLoS ONE"},{"issue":"5","key":"11_CR18","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1086\/228631","volume":"92","author":"P Bonacich","year":"1987","unstructured":"Bonacich, P.: Power and centrality: a family of measures. Am. J. Sociol. 92(5), 1170\u20131182 (1987)","journal-title":"Am. J. Sociol."},{"issue":"1","key":"11_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0378-8733(89)90016-6","volume":"11","author":"K Stephenson","year":"1989","unstructured":"Stephenson, K., Zelen, M.: Rethinking centrality: methods and examples. Soc. Netw. 11(1), 1\u201337 (1989)","journal-title":"Soc. Netw."},{"issue":"4","key":"11_CR20","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1109\/TCBB.2011.147","volume":"9","author":"J Wang","year":"2012","unstructured":"Wang, J., et al.: Identification of essential proteins based on edge clustering coefficient. IEEE\/ACM Trans. Comput. Biol. Bioinform. 9(4), 1070\u20131080 (2012)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"issue":"5 Pt 2","key":"11_CR21","first-page":"056103","volume":"71","author":"E Ernesto","year":"2005","unstructured":"Ernesto, E., Rodr\u00edguez-Vel\u00e1zquez, J.A.: Subgraph centrality in complex networks. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 71(5 Pt 2), 056103 (2005)","journal-title":"Phys. Rev. E Stat. Nonlinear Soft Matter Phys."},{"key":"11_CR22","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/978-3-642-13078-6_11","volume":"6053","author":"M Li","year":"2010","unstructured":"Li, M., et al.: Essential proteins discovery from weighted protein interaction networks. Bioinform. Res. Appl. Proc. 6053, 89\u2013100 (2010)","journal-title":"Bioinform. Res. Appl. Proc."},{"issue":"1","key":"11_CR23","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1752-0509-6-15","volume":"6","author":"M Li","year":"2012","unstructured":"Li, M., et al.: A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. BMC Syst. Biol. 6(1), 15 (2012)","journal-title":"BMC Syst. Biol."},{"issue":"2","key":"11_CR24","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1109\/TCBB.2013.2295318","volume":"11","author":"X Tang","year":"2014","unstructured":"Tang, X., et al.: Predicting essential proteins based on weighted degree centrality. IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB) 11(2), 407\u2013418 (2014)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB)"},{"issue":"2","key":"11_CR25","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1109\/TCBB.2014.2338317","volume":"12","author":"W Peng","year":"2015","unstructured":"Peng, W., et al.: UDoNC: an algorithm for identifying essential proteins based on protein domains and protein-protein interaction networks. IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB) 12(2), 276\u2013288 (2015)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform. (TCBB)"},{"issue":"1","key":"11_CR26","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/1752-0509-6-87","volume":"6","author":"W Peng","year":"2012","unstructured":"Peng, W., et al.: Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. BMC Syst. Biol. 6(1), 87 (2012)","journal-title":"BMC Syst. Biol."},{"issue":"3","key":"11_CR27","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1109\/TNB.2018.2842219","volume":"17","author":"J Zhong","year":"2018","unstructured":"Zhong, J., et al.: XGBFEMF: an XGBoost-based framework for essential protein prediction. IEEE Trans. Nanobioscience 17(3), 243\u2013250 (2018)","journal-title":"IEEE Trans. Nanobioscience"},{"issue":"12","key":"11_CR28","doi-asserted-by":"publisher","first-page":"1758","DOI":"10.1093\/bioinformatics\/btx055","volume":"33","author":"FB Guo","year":"2017","unstructured":"Guo, F.B., et al.: Accurate prediction of human essential genes using only nucleotide composition and association information. Bioinformatics 33(12), 1758\u20131764 (2017)","journal-title":"Bioinformatics"},{"key":"11_CR29","doi-asserted-by":"crossref","unstructured":"Grover, A., Leskovec, J.: node2vec: scalable feature learning for networks. In: KDD, pp. 855\u2013864 (2016)","DOI":"10.1145\/2939672.2939754"},{"key":"11_CR30","unstructured":"Mikolov, T., et al.: Distributed representations of words and phrases and their compositionality. In: International Conference on Neural Information Processing Systems (2013)"},{"issue":"13","key":"11_CR31","doi-asserted-by":"publisher","first-page":"2271","DOI":"10.1093\/bioinformatics\/bty070","volume":"34","author":"J Wu","year":"2018","unstructured":"Wu, J., et al.: WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. Bioinformatics 34(13), 2271\u20132282 (2018)","journal-title":"Bioinformatics"},{"key":"11_CR32","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1186\/1471-2105-10-290","volume":"10","author":"ML Acencio","year":"2009","unstructured":"Acencio, M.L., Lemke, N.: Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics 10, 290 (2009)","journal-title":"BMC Bioinformatics"},{"issue":"15","key":"11_CR33","doi-asserted-by":"publisher","first-page":"1945","DOI":"10.1093\/bioinformatics\/btm287","volume":"23","author":"J Liao","year":"2007","unstructured":"Liao, J., Chin, K.: Logistic regression for disease classification using microarray data: model selection in a large p and small n case. Bioinformatics 23(15), 1945\u20131951 (2007)","journal-title":"Bioinformatics"},{"issue":"1","key":"11_CR34","doi-asserted-by":"publisher","first-page":"e86805","DOI":"10.1371\/journal.pone.0086805","volume":"9","author":"J Cheng","year":"2014","unstructured":"Cheng, J., et al.: Training set selection for the prediction of essential genes. PLoS ONE 9(1), e86805 (2014)","journal-title":"PLoS ONE"},{"issue":"8","key":"11_CR35","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1021\/pr060167c","volume":"5","author":"C Kuo-Chen","year":"2006","unstructured":"Kuo-Chen, C., Hong-Bin, S.: Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers. J. Proteome Res. 5(8), 1888\u20131897 (2006)","journal-title":"J. Proteome Res."},{"issue":"5","key":"11_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2010-11-5-r53","volume":"11","author":"G Wu","year":"2010","unstructured":"Wu, G., Feng, X., Stein, L.: A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11(5), 1\u201323 (2010)","journal-title":"Genome Biol."},{"issue":"1","key":"11_CR37","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/nmeth.4083","volume":"14","author":"T Li","year":"2016","unstructured":"Li, T., et al.: A scored human protein-protein interaction network to catalyze genomic interpretation. Nat. Methods 14(1), 61 (2016)","journal-title":"Nat. Methods"},{"key":"11_CR38","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.biosystems.2014.11.005","volume":"127","author":"Y Tang","year":"2015","unstructured":"Tang, Y., et al.: CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks. Biosystems 127, 67\u201372 (2015)","journal-title":"Biosystems"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-20242-2_11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T13:18:02Z","timestamp":1710335882000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-20242-2_11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030202415","9783030202422"],"references-count":38,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-20242-2_11","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"9 May 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"ISBRA","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Symposium on Bioinformatics Research and Applications","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Barcelona","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"3 June 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 June 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"15","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"isbra2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/alan.cs.gsu.edu\/isbra19\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}