{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T19:39:05Z","timestamp":1743017945242,"version":"3.40.3"},"publisher-location":"Cham","reference-count":35,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319949673"},{"type":"electronic","value":"9783319949680"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"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":[[2018]]},"DOI":"10.1007\/978-3-319-94968-0_28","type":"book-chapter","created":{"date-parts":[[2018,7,12]],"date-time":"2018-07-12T14:13:51Z","timestamp":1531404831000},"page":"287-298","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Prediction of Type III Secreted Effectors Based on Word Embeddings for Protein Sequences"],"prefix":"10.1007","author":[{"given":"Xiaofeng","family":"Fu","sequence":"first","affiliation":[]},{"given":"Yiqun","family":"Xiao","sequence":"additional","affiliation":[]},{"given":"Yang","family":"Yang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,7,13]]},"reference":[{"issue":"7119","key":"28_CR1","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/nature05272","volume":"444","author":"JE Gal\u00e1n","year":"2006","unstructured":"Gal\u00e1n, J.E., Wolf-Wat, H.: Protein delivery into eukaryotic cells by type III secretion machines. Nature 444(7119), 567 (2006)","journal-title":"Nature"},{"issue":"6","key":"28_CR2","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/j.chom.2009.04.008","volume":"5","author":"JE Gal\u00e1n","year":"2009","unstructured":"Gal\u00e1n, J.E.: Common themes in the design and function of bacterial effectors. Cell Host Microbe 5(6), 571\u2013579 (2009)","journal-title":"Cell Host Microbe"},{"issue":"1\u20133","key":"28_CR3","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.bbamcr.2004.03.011","volume":"1694","author":"SY He","year":"2004","unstructured":"He, S.Y., Nomura, K., Whittam, T.S.: Type III protein secretion mechanism in mammalian and plant pathogens. Biochimica et Biophysica Acta (BBA)-Mol. Cell Res. 1694(1\u20133), 181\u2013206 (2004)","journal-title":"Biochimica et Biophysica Acta (BBA)-Mol. Cell Res."},{"issue":"11","key":"28_CR4","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nrmicro1526","volume":"4","author":"GR Cornelis","year":"2006","unstructured":"Cornelis, G.R.: The type III secretion injectisome. Nat. Rev. Microbiol. 4(11), 811 (2006)","journal-title":"Nat. Rev. Microbiol."},{"issue":"1","key":"28_CR5","doi-asserted-by":"publisher","first-page":"S47","DOI":"10.1186\/1471-2105-11-S1-S47","volume":"11","author":"Y Yang","year":"2010","unstructured":"Yang, Y., Zhao, J., Morgan, R.L., Ma, W., Jiang, T.: Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinform. 11(1), S47 (2010)","journal-title":"BMC Bioinform."},{"issue":"S\u20137","key":"28_CR6","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-11-S7-S4","volume":"11","author":"D Tay","year":"2010","unstructured":"Tay, D., Govindarajan, K.R., Khan, A.M., Ong, T., Samad, H.M., Soh, W., Tong, M., Zhang, F., Tan, T.W.: T3SEdb: data warehousing of virulence effectors secreted by the bacterial type III secretion system. BMC Bioinform. 11(S\u20137), S4 (2010)","journal-title":"BMC Bioinform."},{"issue":"1","key":"28_CR7","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/1471-2105-13-66","volume":"13","author":"Y Wang","year":"2012","unstructured":"Wang, Y., Huang, H., Sun, M., Zhang, Q., Guo, D.: T3DB: an integrated database for bacterial type III secretion system. BMC Bioinform. 13(1), 66 (2012)","journal-title":"BMC Bioinform."},{"issue":"12","key":"28_CR8","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/nrg3748","volume":"15","author":"DS Guttman","year":"2014","unstructured":"Guttman, D.S., McHardy, A.C., Schulze-Lefert, P.: Microbial genome-enabled insights into plant-microorganism interactions. Nat. Rev. Genet. 15(12), 797 (2014)","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"28_CR9","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1128\/IAI.00537-10","volume":"79","author":"JE McDermott","year":"2011","unstructured":"McDermott, J.E., Corrigan, A., Peterson, E., Oehmen, C., Niemann, G., Cambronne, E.D., Sharp, D., Adkins, J.N., Samudrala, R., Heffron, F.: Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect. Immun. 79(1), 23\u201332 (2011)","journal-title":"Infect. Immun."},{"issue":"12","key":"28_CR10","doi-asserted-by":"publisher","first-page":"2293","DOI":"10.1016\/j.patcog.2005.11.012","volume":"39","author":"D-S Huang","year":"2006","unstructured":"Huang, D.-S., Zhao, X.-M., Huang, G.-B., Cheung, Y.-M.: Classifying protein sequences using hydropathy blocks. Pattern Recogn. 39(12), 2293\u20132300 (2006)","journal-title":"Pattern Recogn."},{"issue":"02","key":"28_CR11","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1142\/S021800140600465X","volume":"20","author":"X-M Zhao","year":"2006","unstructured":"Zhao, X.-M., Du, J.-X., Wang, H.-Q., Zhu, Y., Li, Y.: A new technique for selecting features from protein sequences. Int. J. Pattern Recognit Artif. Intell. 20(02), 271\u2013283 (2006)","journal-title":"Int. J. Pattern Recognit Artif. Intell."},{"issue":"8","key":"28_CR12","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1016\/j.neunet.2005.07.002","volume":"18","author":"X-M Zhao","year":"2005","unstructured":"Zhao, X.-M., Cheung, Y.-M., Huang, D.-S.: A novel approach to extracting features from motif content and protein composition for protein sequence classification. Neural Netw. 18(8), 1019\u20131028 (2005)","journal-title":"Neural Netw."},{"issue":"4","key":"28_CR13","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1504\/IJDMB.2014.064894","volume":"10","author":"Y Yang","year":"2014","unstructured":"Yang, Y., Qi, S.: A new feature selection method for computational prediction of type III secreted effectors. Int. J. Data Min. Bioinform. 10(4), 440\u2013454 (2014)","journal-title":"Int. J. Data Min. Bioinform."},{"issue":"6","key":"28_CR14","doi-asserted-by":"publisher","first-page":"e5917","DOI":"10.1371\/journal.pone.0005917","volume":"4","author":"M L\u00f6wer","year":"2009","unstructured":"L\u00f6wer, M., Schneider, G.: Prediction of type III secretion signals in genomes of gram-negative bacteria. PLoS ONE 4(6), e5917 (2009)","journal-title":"PLoS ONE"},{"issue":"6","key":"28_CR15","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1093\/bioinformatics\/btr021","volume":"27","author":"Y Wang","year":"2011","unstructured":"Wang, Y., Zhang, Q., Sun, M., Guo, D.: High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 27(6), 777\u2013784 (2011)","journal-title":"Bioinformatics"},{"key":"28_CR16","doi-asserted-by":"publisher","first-page":"34516","DOI":"10.1038\/srep34516","volume":"6","author":"T Goldberg","year":"2016","unstructured":"Goldberg, T., Rost, B., Bromberg, Y.: Computational prediction shines light on type III secretion origins. Sci. Rep. 6, 34516 (2016)","journal-title":"Sci. Rep."},{"key":"28_CR17","volume-title":"Bioinformatics: The Machine Learning Approach","author":"P Baldi","year":"2001","unstructured":"Baldi, P., Brunak, S.: Bioinformatics: The Machine Learning Approach. MIT Press, Cambridge (2001)"},{"key":"28_CR18","unstructured":"Mikolov, T., Chen, K., Corrado, G., Dean, J.: Efficient estimation of word representations in vector space. arXiv preprint \narXiv:1301.3781\n\n (2013)"},{"key":"28_CR19","unstructured":"Klein-Seetharaman, J., Reddy, R.: Biological language modeling: convergence of computational linguistics and biological chemistry. Converg. Technol. Improv. Hum. Perform. 378 (2002)"},{"issue":"11","key":"28_CR20","doi-asserted-by":"publisher","first-page":"e0141287","DOI":"10.1371\/journal.pone.0141287","volume":"10","author":"E Asgari","year":"2015","unstructured":"Asgari, E., Mofrad, M.R.K.: Continuous distributed representation of biological sequences for deep proteomics and genomics. PLoS ONE 10(11), e0141287 (2015)","journal-title":"PLoS ONE"},{"key":"28_CR21","unstructured":"Mikolov, T., Sutskever, I., Chen, K., Corrado, G., Dean, J.: Distributed representations of words and phrases and their compositionality. CoRR, abs\/1310.4546 (2013)"},{"key":"28_CR22","doi-asserted-by":"crossref","unstructured":"Jehl, M.-A., Arnold, R., Rattei, T.: Effective\u2014a database of predicted secreted bacterial proteins. Nucleic Acids Res. 39(Suppl$$\\_1$$), D591\u2013D595 (2010)","DOI":"10.1093\/nar\/gkq1154"},{"key":"28_CR23","doi-asserted-by":"publisher","first-page":"bav064","DOI":"10.1093\/database\/bav064","volume":"2015","author":"X Dong","year":"2015","unstructured":"Dong, X., Lu, X., Zhang, Z.: Bean 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. Database 2015, bav064 (2015)","journal-title":"Database"},{"issue":"13","key":"28_CR24","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","volume":"22","author":"W Li","year":"2006","unstructured":"Li, W., Godzik, A.: CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13), 1658\u20131659 (2006)","journal-title":"Bioinformatics"},{"issue":"1","key":"28_CR25","doi-asserted-by":"publisher","first-page":"S36","DOI":"10.1186\/1471-2105-10-S1-S36","volume":"10","author":"D Song","year":"2009","unstructured":"Song, D., Yang, Y., Yu, B., Zheng, B., Deng, Z., Lu, B.-L., Chen, X., Jiang, T.: Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. BMC Bioinform. 10(1), S36 (2009)","journal-title":"BMC Bioinform."},{"issue":"1","key":"28_CR26","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/1471-2105-9-57","volume":"9","author":"X-M Zhao","year":"2008","unstructured":"Zhao, X.-M., Wang, Y., Chen, L., Aihara, K.: Gene function prediction using labeled and unlabeled data. BMC Bioinform. 9(1), 57 (2008)","journal-title":"BMC Bioinform."},{"issue":"4","key":"28_CR27","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1002\/prot.21870","volume":"70","author":"X-M Zhao","year":"2008","unstructured":"Zhao, X.-M., Li, X., Chen, L., Aihara, K.: Protein classification with imbalanced data. Proteins: Struct. Funct. Bioinform. 70(4), 1125\u20131132 (2008)","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"4","key":"28_CR28","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1002\/prot.20373","volume":"58","author":"BYM Cheng","year":"2005","unstructured":"Cheng, B.Y.M., Carbonell, J.G., Klein-Seetharaman, J.: Protein classification based on text document classification techniques. Proteins: Struct. Funct. Bioinform. 58(4), 955\u2013970 (2005)","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"20","key":"28_CR29","doi-asserted-by":"publisher","first-page":"2655","DOI":"10.1093\/bioinformatics\/btp500","volume":"25","author":"Q Dong","year":"2009","unstructured":"Dong, Q., Zhou, S., Guan, J.: A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation. Bioinform. 25(20), 2655\u20132662 (2009)","journal-title":"Bioinform."},{"issue":"9","key":"28_CR30","doi-asserted-by":"publisher","first-page":"3025","DOI":"10.1093\/nar\/gkn159","volume":"36","author":"Y Guo","year":"2008","unstructured":"Guo, Y., Yu, L., Wen, Z., Li, M.: Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res. 36(9), 3025\u20133030 (2008)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"28_CR31","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1186\/1471-2105-9-510","volume":"9","author":"B Liu","year":"2008","unstructured":"Liu, B., Wang, X., Lin, L., Dong, Q., Wang, X.: A discriminative method for protein remote homology detection and fold recognition combining top-n-grams and latent semantic analysis. BMC Bioinform. 9(1), 510 (2008)","journal-title":"BMC Bioinform."},{"issue":"3","key":"28_CR32","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1002\/prot.1035","volume":"43","author":"K-C Chou","year":"2001","unstructured":"Chou, K.-C.: Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins: Struct. Funct. Bioinform. 43(3), 246\u2013255 (2001)","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"1","key":"28_CR33","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1093\/bioinformatics\/bth466","volume":"21","author":"K-C Chou","year":"2004","unstructured":"Chou, K.-C.: Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21(1), 10\u201319 (2004)","journal-title":"Bioinformatics"},{"issue":"3","key":"28_CR34","doi-asserted-by":"publisher","first-page":"3495","DOI":"10.3390\/ijms15033495","volume":"15","author":"P Du","year":"2014","unstructured":"Du, P., Gu, S., Jiao, Y.: PseAAC-general: fast building various modes of general form of chous pseudo-amino acid composition for large-scale protein datasets. Int. J. Mol. Sci. 15(3), 3495\u20133506 (2014)","journal-title":"Int. J. Mol. Sci."},{"issue":"W1","key":"28_CR35","doi-asserted-by":"publisher","first-page":"W65","DOI":"10.1093\/nar\/gkv458","volume":"43","author":"B Liu","year":"2015","unstructured":"Liu, B., Liu, F., Wang, X., Chen, J., Fang, L., Chou, K.-C.: Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. Nucleic Acids Res. 43(W1), W65\u2013W71 (2015)","journal-title":"Nucleic Acids Res."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-94968-0_28","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,6]],"date-time":"2020-02-06T05:03:37Z","timestamp":1580965417000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-94968-0_28"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9783319949673","9783319949680"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-94968-0_28","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2018]]},"assertion":[{"value":"13 July 2018","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":"Beijing","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"China","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2018","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8 June 2018","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"11 June 2018","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"14","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"isbra2018","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/alan.cs.gsu.edu\/isbra18\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}