{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T02:48:23Z","timestamp":1790736503386,"version":"4.1.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2018,11,1]],"date-time":"2018-11-01T00:00:00Z","timestamp":1541030400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Key R&D Program of China","award":["SQ2018YFC090002"],"award-info":[{"award-number":["SQ2018YFC090002"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61701340"],"award-info":[{"award-number":["61701340"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61702361"],"award-info":[{"award-number":["61702361"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61771331"],"award-info":[{"award-number":["61771331"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP110200333"],"award-info":[{"award-number":["LP110200333"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP120104460"],"award-info":[{"award-number":["DP120104460"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["4909809"],"award-info":[{"award-number":["4909809"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI111965"],"award-info":[{"award-number":["R01 AI111965"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001779","name":"Monash University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001779","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005683","name":"Kyoto University","doi-asserted-by":"publisher","award":["2018\u201328"],"award-info":[{"award-number":["2018\u201328"]}],"id":[{"id":"10.13039\/501100005683","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1093\/bib\/bby107","type":"journal-article","created":{"date-parts":[[2018,10,6]],"date-time":"2018-10-06T07:20:45Z","timestamp":1538810445000},"source":"Crossref","is-referenced-by-count":58,"title":["Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1444-190X","authenticated-orcid":false,"given":"Leyi","family":"Wei","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Tianjin University, Tianjin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Tianjin University, Tianjin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"},{"name":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, Clayton, VIC, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"},{"name":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, Clayton, VIC, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ran","family":"Su","sequence":"additional","affiliation":[{"name":"School of Computer Software, Tianjin University, Tianjin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Tianjin University, Tianjin, China"},{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,10,31]]},"reference":[{"key":"key\n\t\t\t\t2019012509272681600_ref1","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.micro.55.1.165","article-title":"Quorum sensing in bacteria","volume":"55","author":"Miller","year":"2001","journal-title":"Annu Rev Microbiol"},{"key":"key\n\t\t\t\t2019012509272681600_ref2","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev.cellbio.21.012704.131001","article-title":"Quorum sensing: cell-to-cell communication in bacteria","volume":"21","author":"Waters","year":"2005","journal-title":"Annu Rev Cell Dev Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref3","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/S1369-5274(99)00025-9","article-title":"How bacteria talk to each other: regulation of gene expression by quorum sensing","volume":"2","author":"Bassler","year":"1999","journal-title":"Curr Opin Microbiol"},{"key":"key\n\t\t\t\t2019012509272681600_ref4","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/415545a","article-title":"Structural identification of a bacterial quorum-sensing signal containing boron","volume":"415","author":"Chen","year":"2002","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019012509272681600_ref5","doi-asserted-by":"crossref","first-page":"D655","DOI":"10.1093\/nar\/gks1137","article-title":"Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides","volume":"41","author":"Wynendaele","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref6","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/jb.176.2.269-275.1994","article-title":"Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators","volume":"176","author":"Fuqua","year":"1994","journal-title":"J Bacteriol"},{"key":"key\n\t\t\t\t2019012509272681600_ref7","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1128\/JB.104.1.313-322.1970","article-title":"Cellular control of the synthesis and activity of the bacterial luminescent system","volume":"104","author":"Nealson","year":"1970","journal-title":"J Bacteriol"},{"key":"key\n\t\t\t\t2019012509272681600_ref8","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1046\/j.1365-2958.1997.4251782.x","article-title":"Quorum sensing by peptide pheromones and two-component signal-transduction systems in Gram-positive bacteria","volume":"24","author":"Kleerebezem","year":"1997","journal-title":"Mol Microbiol"},{"key":"key\n\t\t\t\t2019012509272681600_ref9","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1084\/jem.54.5.681","article-title":"In vitro transformation of pneumococcal types: I. A technique for inducing transformation of pneumococcal types in vitro","volume":"54","author":"Dawson","year":"1931","journal-title":"J Exp Med"},{"key":"key\n\t\t\t\t2019012509272681600_ref10","first-page":"1","volume-title":"Cell-cell Signaling in Bacteria","author":"Dunny","year":"1999"},{"key":"key\n\t\t\t\t2019012509272681600_ref11","doi-asserted-by":"crossref","first-page":"11229","DOI":"10.1073\/pnas.96.20.11229","article-title":"Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa","volume":"96","author":"Pesci","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t2019012509272681600_ref12","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.gpb.2013.01.004","article-title":"Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency","volume":"11","author":"Ma","year":"2013","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref13","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gkv458","article-title":"Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences","volume":"43","author":"Liu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref14","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1142\/S0219720005001004","article-title":"Minimum redundancy feature selection from microarray gene expression data","volume":"3","author":"Ding","year":"2005","journal-title":"J Bioinform Comput Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref15","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1109\/TPAMI.2005.159","article-title":"Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy","volume":"27","author":"Peng","year":"2005","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"key\n\t\t\t\t2019012509272681600_ref16","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1109\/T-C.1971.223410","article-title":"A direct method of nonparametric measurement selection","volume":"100","author":"Whitney","year":"1971","journal-title":"IEEE Trans Comput"},{"key":"key\n\t\t\t\t2019012509272681600_ref17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0120066","article-title":"Prediction and analysis of quorum sensing peptides based on sequence features","volume":"10","author":"Rajput","year":"2015","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019012509272681600_ref18","doi-asserted-by":"crossref","first-page":"D655","DOI":"10.1093\/nar\/gks1137","article-title":"Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides","volume":"41","author":"Wynendaele","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref19","doi-asserted-by":"crossref","first-page":"W783","DOI":"10.1093\/nar\/gki470","article-title":"GoPubMed: exploring PubMed with the gene ontology","volume":"33","author":"Doms","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0016968","article-title":"Connecting peptide physicochemical and antimicrobial properties by a rational prediction model","volume":"6","author":"Torrent","year":"2011","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019012509272681600_ref21","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random Forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach Learn"},{"key":"key\n\t\t\t\t2019012509272681600_ref22","first-page":"8309253","article-title":"Prediction of G-protein-coupled receptors with SVM-Prot features and random forest","volume":"2016","author":"Liao","year":"2016","journal-title":"Forensic Sci"},{"key":"key\n\t\t\t\t2019012509272681600_ref23","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1093\/bioinformatics\/btu852","article-title":"GlycoMine: a machine learning-based approach for predicting N-, C-and O-linked glycosylation in the human proteome","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref24","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.jtbi.2018.01.023","article-title":"PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework","volume":"443","author":"Song","year":"2018","journal-title":"J Theor Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref25","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1186\/s12864-017-4128-1","article-title":"SkipCPP-Pred: an improved and promising sequence-based predictor for predicting cell-penetrating peptides","volume":"18","author":"Wei","year":"2017","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t2019012509272681600_ref26","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1021\/acs.jproteome.7b00019","article-title":"CPPred-RF: a sequence-based predictor for identifying cell-penetrating peptides and their uptake efficiency","volume":"16","author":"Wei","year":"2017","journal-title":"J Proteome Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref27","doi-asserted-by":"crossref","first-page":"289","DOI":"10.2174\/157016461104150121115154","article-title":"Exploratory predicting protein folding model with random forest and hybrid features","volume":"11","author":"Zhao","year":"2014","journal-title":"Curr Proteomics"},{"key":"key\n\t\t\t\t2019012509272681600_ref28","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/bioinformatics\/btx579","article-title":"iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC","volume":"34","author":"Liu","year":"2018","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref29","article-title":"iRO-3wPseKNC: Identify DNA replication origins by three-window-based PseKNC","author":"Liu","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref30","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1186\/s13059-018-1512-3","article-title":"Alternative splicing links histone modifications to stem cell fate decision","volume":"19","author":"Xu","year":"2018","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref31","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1145\/1656274.1656278","article-title":"The WEKA data mining software: an update","volume":"11","author":"Hall","year":"2009","journal-title":"ACM SIGKDD Explorations Newsletter"},{"key":"key\n\t\t\t\t2019012509272681600_ref32","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.1093\/bioinformatics\/bty140","article-title":"iFeature: a python package and web server for features extraction and selection from protein and peptide sequences","volume":"32","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref33","article-title":"iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites","author":"Song","year":"2018","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t2019012509272681600_ref34","doi-asserted-by":"crossref","first-page":"8700","DOI":"10.1073\/pnas.92.19.8700","article-title":"Prediction of protein folding class using global description of amino acid sequence","volume":"92","author":"Dubchak","year":"1995","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t2019012509272681600_ref35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1109\/INDCON.2011.6139332","article-title":"Composition, transition and distribution (CTD)\u2014a dynamic feature for predictions based on hierarchical structure of cellular sorting","volume-title":"India Conference (INDICON), 2011 Annual IEEE,","author":"Govindan","year":"2011"},{"key":"key\n\t\t\t\t2019012509272681600_ref36","article-title":"Hierarchical classification of protein folds using a novel ensemble classifier","volume":"8","author":"Lin","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019012509272681600_ref37","doi-asserted-by":"crossref","DOI":"10.1155\/2013\/686090","article-title":"An approach for identifying cytokines based on a novel ensemble classifier","volume":"2013","author":"Zou","year":"2013","journal-title":"Biomed Res Int"},{"key":"key\n\t\t\t\t2019012509272681600_ref38","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/bty451","article-title":"ACPred-FL: a sequence-based predictor based on effective feature representation to improve the prediction of anti-cancer peptides","author":"Wei","year":"2018","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref39","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/bioinformatics\/btm270","article-title":"Predicting functionally important residues from sequence conservation","volume":"23","author":"Capra","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref40","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1109\/TNB.2017.2661756","article-title":"PhosPred-RF: a novel sequence-based predictor for phosphorylation sites using sequential information only","volume":"16","author":"Wei","year":"2017","journal-title":"IEEE Trans Nanobioscience"},{"key":"key\n\t\t\t\t2019012509272681600_ref41","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1479-5876-11-74","article-title":"In silico approaches for designing highly effective cell penetrating peptides","volume":"11","author":"Gautam","year":"2013","journal-title":"J Transl Med"},{"key":"key\n\t\t\t\t2019012509272681600_ref42","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1007\/s00726-014-1711-5","article-title":"PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine","volume":"46","author":"Dou","year":"2014","journal-title":"Amino Acids"},{"key":"key\n\t\t\t\t2019012509272681600_ref43","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.neucom.2014.12.123","article-title":"A novel features ranking metric with application to scalable visual and bioinformatics data classification","volume":"173","author":"Zou","year":"2016","journal-title":"Neurocomputing"},{"key":"key\n\t\t\t\t2019012509272681600_ref44","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/s12918-016-0353-5","article-title":"Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy","volume":"10","author":"Zou","year":"2016","journal-title":"BMC Syst Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref45","article-title":"BioSeq-Analysis: a platform for DNA, RNA, and protein sequence analysis based on machine learning approaches","author":"Liu","year":"2018","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t2019012509272681600_ref46","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/bty508","article-title":"iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC","author":"Su","year":"2018","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref47","doi-asserted-by":"crossref","first-page":"957","DOI":"10.7150\/ijbs.24174","article-title":"HBPred: a tool to identify growth hormone-binding proteins","volume":"14","author":"Tang","year":"2018","journal-title":"Int J Biol Sci"},{"key":"key\n\t\t\t\t2019012509272681600_ref48","doi-asserted-by":"crossref","DOI":"10.1089\/cmb.2018.0004","article-title":"iRNA-2OM: a sequence-based predictor for identifying 2\u2032-O-methylation sites in homo sapiens","author":"Yang","year":"2018","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t2019012509272681600_ref49","doi-asserted-by":"crossref","first-page":"883","DOI":"10.7150\/ijbs.24616","article-title":"iRSpot-Pse6NC: identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC","volume":"14","author":"Yang","year":"2018","journal-title":"Int J Biol Sci"},{"key":"key\n\t\t\t\t2019012509272681600_ref50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1109\/TCYB.2018.2863020","article-title":"An evolutionary algorithm based on Minkowski distance for many-objective optimization","author":"Xu","year":"2018","journal-title":"IEEE Trans Cybern"},{"key":"key\n\t\t\t\t2019012509272681600_ref51","article-title":"MOEA\/HD: a multiobjective evolutionary algorithm based on hierarchical decomposition","author":"Xu","year":"2017","journal-title":"IEEE Trans Cybern"},{"key":"key\n\t\t\t\t2019012509272681600_ref52","doi-asserted-by":"crossref","first-page":"77121","DOI":"10.18632\/oncotarget.20365","article-title":"MLACP: machine-learning-based prediction of anticancer peptides","volume":"8","author":"Manavalan","year":"2017","journal-title":"Oncotarget"},{"key":"key\n\t\t\t\t2019012509272681600_ref53","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0106542","article-title":"Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms","volume":"9","author":"Manavalan","year":"2014","journal-title":"PLoS One"},{"issue":"8","key":"key\n\t\t\t\t2019012509272681600_ref54","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1021\/acs.jproteome.8b00148","article-title":"Machine-learning-based prediction of cell-penetrating peptides and their uptake efficiency with improved accuracy","volume":"17","author":"Manavalan","year":"2018","journal-title":"J Proteome Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref55","doi-asserted-by":"crossref","first-page":"12100","DOI":"10.1093\/nar\/gkx870","article-title":"Deep learning of the splicing (epi) genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision","volume":"45","author":"Xu","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref56","doi-asserted-by":"crossref","DOI":"10.1016\/j.artmed.2017.09.003","article-title":"Machine learning and graph analytics in computational biomedicine.","volume":"83","author":"Zou","year":"2017","journal-title":"Artif Intell Med"},{"key":"key\n\t\t\t\t2019012509272681600_ref57","doi-asserted-by":"crossref","DOI":"10.1155\/2017\/5652041","article-title":"Scalable data mining algorithms in computational biology and biomedicine","volume":"2017","author":"Zou","year":"2017","journal-title":"Biomed Res Int"},{"key":"key\n\t\t\t\t2019012509272681600_ref58","doi-asserted-by":"crossref","first-page":"5765","DOI":"10.1038\/srep05765","article-title":"Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features","volume":"4","author":"Li","year":"2014","journal-title":"Sci Rep"},{"key":"key\n\t\t\t\t2019012509272681600_ref59","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/bioinformatics\/btt603","article-title":"Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets","volume":"30","author":"Wang","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref60","doi-asserted-by":"crossref","first-page":"5594","DOI":"10.1093\/nar\/gkt261","article-title":"Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions","volume":"41","author":"Ma","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref61","first-page":"8","article-title":"Prediction of potential disease-associated microRNAs using structural perturbation method","volume":"1","author":"Zeng","year":"2018","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref62","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bby090","article-title":"Sequence clustering in bioinformatics: an empirical study","author":"Zou","year":"2018","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t2019012509272681600_ref63","article-title":"A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction","author":"Liu","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t2019012509272681600_ref64","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1148\/radiology.143.1.7063747","article-title":"The meaning and use of the area under a receiver operating characteristic (ROC) curve","volume":"143","author":"Hanley","year":"1982","journal-title":"Radiology"},{"key":"key\n\t\t\t\t2019012509272681600_ref65","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1093\/bioinformatics\/btt709","article-title":"Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection","volume":"30","author":"Liu","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref66","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1093\/bib\/bbw108","article-title":"A comprehensive review and comparison of different computational methods for protein remote homology detection","volume":"19","author":"Chen","year":"2018","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t2019012509272681600_ref67","first-page":"1","article-title":"iBCE-EL: a new ensemble learning framework for improved linear B-cell epitope prediction","volume":"9","author":"Manavalan","year":"2018","journal-title":"Front Immunol"},{"key":"key\n\t\t\t\t2019012509272681600_ref68","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/btx222","article-title":"SVMQA: support-vector-machine-based protein single-model quality assessment","volume":"33","author":"Manavalan","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref69","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.3389\/fimmu.2018.01783","article-title":"PIP-EL: a new ensemble learning method for improved proinflammatory peptide predictions","volume":"9","author":"Manavalan","year":"2018","journal-title":"Front Immunol"},{"key":"key\n\t\t\t\t2019012509272681600_ref70","doi-asserted-by":"crossref","first-page":"476","DOI":"10.3389\/fmicb.2018.00476","article-title":"PVP-SVM: sequence-based prediction of phage virion proteins using a support vector machine","volume":"9","author":"Manavalan","year":"2018","journal-title":"Front Microbiol"},{"key":"key\n\t\t\t\t2019012509272681600_ref71","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.18632\/oncotarget.23099","article-title":"DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest","volume":"9","author":"Manavalan","year":"2018","journal-title":"Oncotarget"},{"key":"key\n\t\t\t\t2019012509272681600_ref72","doi-asserted-by":"crossref","first-page":"3287","DOI":"10.1021\/ci200206n","article-title":"Protein\u2013protein binding sites prediction by 3D structural similarities","volume":"51","author":"Guo","year":"2011","journal-title":"J Chem Inf Model"},{"key":"key\n\t\t\t\t2019012509272681600_ref73","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1021\/ci5002372","article-title":"Probabilistic models for capturing more physicochemical properties on protein\u2013protein Interface","volume":"54","author":"Guo","year":"2014","journal-title":"J Chem Inf Model"},{"key":"key\n\t\t\t\t2019012509272681600_ref74","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1186\/s12859-016-1253-9","article-title":"Predicting protein\u2013protein interactions via multivariate mutual information of protein sequences","volume":"17","author":"Ding","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref75","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.ins.2017.08.045","article-title":"Identification of drug-target interactions via multiple information integration","volume":"418","author":"Ding","year":"2017","journal-title":"Inform Sci"},{"key":"key\n\t\t\t\t2019012509272681600_ref76","article-title":"Identification of 14-3-3 proteins phosphopeptide-binding specificity using an affinity-based computational approach","volume":"11","author":"Li","year":"2016","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019012509272681600_ref77","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1186\/1471-2105-13-158","article-title":"Protein\u2013protein binding site identification by enumerating the configurations","volume":"13","author":"Guo","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref78","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1021\/acs.jcim.5b00320","article-title":"Identification of protein\u2013protein Interactions by detecting correlated mutation at the interface","volume":"55","author":"Guo","year":"2015","journal-title":"J Chem Inf Model"},{"key":"key\n\t\t\t\t2019012509272681600_ref79","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1093\/bioinformatics\/btt397","article-title":"An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale","volume":"29","author":"Ma","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref80","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1093\/bioinformatics\/btx223","article-title":"DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses","volume":"33","author":"Yang","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012509272681600_ref81","article-title":"A new framework for identifying cis-regulatory motifs in prokaryotes","volume":"39","author":"Li","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019012509272681600_ref82","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1186\/s12864-016-2982-x","article-title":"An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes","volume":"17","author":"Liu","year":"2016","journal-title":"BMC Genomics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/advance-article-pdf\/doi\/10.1093\/bib\/bby107\/26269911\/bby107.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T00:31:16Z","timestamp":1605141076000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/advance-article\/doi\/10.1093\/bib\/bby107\/5152318"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,31]]},"references-count":82,"URL":"https:\/\/doi.org\/10.1093\/bib\/bby107","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,31]]}}}