{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:29:51Z","timestamp":1778635791904,"version":"3.51.4"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,2]]},"DOI":"10.1186\/s12859-018-2017-5","type":"journal-article","created":{"date-parts":[[2018,2,19]],"date-time":"2018-02-19T19:51:50Z","timestamp":1519069910000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Improving prediction of heterodimeric protein complexes using combination with pairwise kernel"],"prefix":"10.1186","volume":"19","author":[{"given":"Peiying","family":"Ruan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morihiro","family":"Hayashida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Philippe","family":"Vert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,2,19]]},"reference":[{"key":"2017_CR1","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"AC Gavin","year":"2006","unstructured":"Gavin AC, Aloy P, Grandi P, Krause R, Boesche M. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006; 440:631\u20136.","journal-title":"Nature"},{"issue":"3","key":"2017_CR2","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1093\/nar\/gkn1005","volume":"37","author":"S Pu","year":"2009","unstructured":"Pu S, Wong J, Turner B, Cho E, Wodak S. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009; 37(3):825\u201331.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2017_CR3","first-page":"D169","volume":"34","author":"HW Mewes","year":"2004","unstructured":"Mewes HW, Amid C, Arnold R, Frishman D, Guldener U. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2004; 34(Database issue):D169\u201372.","journal-title":"Nucleic Acids Res"},{"issue":"6868","key":"2017_CR4","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","volume":"415","author":"Y Ho","year":"2002","unstructured":"Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L. Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry. Nature. 2002; 415(6868):180\u20133.","journal-title":"Nature"},{"issue":"7084","key":"2017_CR5","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"AC Gavin","year":"2006","unstructured":"Gavin AC, Aloy P, Grandi P, Krause R, Boesche M. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006; 440(7084):631\u20136.","journal-title":"Nature"},{"issue":"7084","key":"2017_CR6","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X. Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature. 2006; 440(7084):637\u201343.","journal-title":"Nature"},{"issue":"6770","key":"2017_CR7","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield T, Judson R. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000; 403(6770):623\u20137.","journal-title":"Nature"},{"issue":"8","key":"2017_CR8","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","volume":"98","author":"T Ito","year":"2001","unstructured":"Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M. A comprehensive two-hybrid analyzes to explore the yeast protein interactive. Proc Natl Acad Sci USA. 2001; 98(8):4569\u201374.","journal-title":"Proc Natl Acad Sci USA"},{"key":"2017_CR9","volume-title":"The yeast two-hybrid system","author":"PL Bartel","year":"1997","unstructured":"Bartel PL, Fields S. The yeast two-hybrid system. New York: Oxford University Press; 1997."},{"issue":"6","key":"2017_CR10","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1002\/pmic.200600448","volume":"7","author":"L Kiemer","year":"2007","unstructured":"Kiemer L, Costa S, Ueffing M, Cesareni G. WI-PHI: A weighted yeast interactive enriched for direct physical interactions. Proteomics. 2007; 7(6):932\u201343.","journal-title":"Proteomics"},{"issue":"Database issue","key":"2017_CR11","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006; 34(Database issue):D535\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2017_CR12","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","volume":"513","author":"A Zanzoni","year":"2002","unstructured":"Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M. MINT: a Molecular INTeration database. FEBS Lett. 2002; 513(1):135\u201340.","journal-title":"FEBS Lett"},{"issue":"Database issue","key":"2017_CR13","doi-asserted-by":"publisher","first-page":"D418","DOI":"10.1093\/nar\/gki051","volume":"33","author":"C Alfarano","year":"2005","unstructured":"Alfarano C, Andrade C, Anthony K, Bahroos N, Bajec M. The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 2005; 33(Database issue):D418\u201324.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2017_CR14","doi-asserted-by":"publisher","first-page":"2615","DOI":"10.1039\/c1mb05120b","volume":"7","author":"A Sapkota","year":"2011","unstructured":"Sapkota A, Liu X, Zhao XM, Cao Y, Liu J. DIPOS: database of interacting proteins in Oryza sativa. Mol BioSyst. 2011; 7(9):2615\u201321.","journal-title":"Mol BioSyst"},{"issue":"10","key":"2017_CR15","doi-asserted-by":"publisher","first-page":"4714","DOI":"10.1021\/pr900415b","volume":"8","author":"XM Zhao","year":"2009","unstructured":"Zhao XM, Zhang XW, Tang WH, Chen L. FPPI: Fusarium graminearum protein-protein interaction database. J Proteome Res. 2009; 8(10):4714\u201321.","journal-title":"J Proteome Res"},{"issue":"7","key":"2017_CR16","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"A Enright","year":"2002","unstructured":"Enright A, Dongen SV, Ouzounis C. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002; 30(7):1575\u201384.","journal-title":"Nucleic Acids Res"},{"key":"2017_CR17","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1471-2105-4-2","volume":"4","author":"GD Bader","year":"2003","unstructured":"Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003; 4:2.","journal-title":"BMC Bioinformatics"},{"issue":"15","key":"2017_CR18","doi-asserted-by":"publisher","first-page":"1891","DOI":"10.1093\/bioinformatics\/btp311","volume":"25","author":"G Liu","year":"2009","unstructured":"Liu G, Wong L, Chua HN. Complex discovery from weighted PPI networks. Bioinformatics. 2009; 25(15):1891\u20137.","journal-title":"Bioinformatics"},{"issue":"3","key":"2017_CR19","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1142\/S0219720008003497","volume":"6","author":"H Chua","year":"2008","unstructured":"Chua H, Ning K, Sung WK, Leong H, Wong L. Using indirect protein-protein interactions for protein complex prediction. J Bioinforma Comput Biol. 2008; 6(3):435\u201366.","journal-title":"J Bioinforma Comput Biol"},{"issue":"8","key":"2017_CR20","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1093\/bioinformatics\/btl039","volume":"22","author":"B Adamcsek","year":"2006","unstructured":"Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics. 2006; 22(8):1021\u20133.","journal-title":"Bioinformatics"},{"issue":"17","key":"2017_CR21","doi-asserted-by":"publisher","first-page":"3013","DOI":"10.1093\/bioinformatics\/bth351","volume":"20","author":"A King","year":"2004","unstructured":"King A, Prulj N, Jurisical I. Protein complex prediction via cost-based clustering. Bioinformatics. 2004; 20(17):3013\u201320.","journal-title":"Bioinformatics"},{"issue":"3","key":"2017_CR22","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1109\/TCBB.2010.78","volume":"8","author":"J Feng","year":"2011","unstructured":"Feng J, Jiang R, Jiang T. A Max-Flow-Based approach to the identification of protein complexes Using protein interaction and microarray data. IEEE\/ACM Trans Comput Biol Bioinforma. 2011; 8(3):621\u201334.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"issue":"13","key":"2017_CR23","doi-asserted-by":"publisher","first-page":"i250","DOI":"10.1093\/bioinformatics\/btn164","volume":"24","author":"Y Qi","year":"2008","unstructured":"Qi Y, Balem F, Faloutsos C, Klein-Seetharaman J, Bar-Joseph Z. Protein complex identification by supervised graph local clustering. Bioinformatics. 2008; 24(13):i250\u20138.","journal-title":"Bioinformatics"},{"key":"2017_CR24","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1186\/1471-2105-10-283","volume":"10","author":"K Macropol","year":"2009","unstructured":"Macropol K, Can T, Singh A. RRW: repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinformatics. 2009; 10:283.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"2017_CR25","doi-asserted-by":"publisher","first-page":"S14","DOI":"10.1186\/1477-5956-9-S1-S14","volume":"9","author":"O Maruyama","year":"2011","unstructured":"Maruyama O, Chihara A. NWE: Node-weighted expansion for protein complex prediction using random walk distances. Proteome Sci. 2011; 9(Suppl 1):S14.","journal-title":"Proteome Sci"},{"key":"2017_CR26","volume-title":"ACM Conference on Bioinformatics, Computational Biology and Biomedicine","author":"O Maruyama","year":"2011","unstructured":"Maruyama O. Heterodimeric protein complex identification. In: ACM Conference on Bioinformatics, Computational Biology and Biomedicine. New York: ACM: 2011. p. 499\u2013501."},{"issue":"6","key":"2017_CR27","doi-asserted-by":"publisher","first-page":"e65265","DOI":"10.1371\/journal.pone.0065265","volume":"8","author":"P Ruan","year":"2013","unstructured":"Ruan P, Hayashida M, Maruyama O, Akutsu T. Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PLoS ONE. 2013; 8(6):e65265.","journal-title":"PLoS ONE"},{"issue":"Suppl 5","key":"2017_CR28","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1752-0509-8-S5-S3","volume":"8","author":"CH Yong","year":"2014","unstructured":"Yong CH, Maruyama O, Wong L. Discovery of small protein complexes from PPI networks with size-specific supervised weighting. BMC Syst Biol. 2014; 8(Suppl 5):S3.","journal-title":"BMC Syst Biol"},{"issue":"9","key":"2017_CR29","doi-asserted-by":"publisher","first-page":"2088","DOI":"10.1002\/prot.24564","volume":"82","author":"K Yugandhar","year":"2014","unstructured":"Yugandhar K, Michael Gromiha M. Feature selection and classification of protein\u2013protein complexes based on their binding affinities using machine learning approaches. Proteins. 2014; 82(9):2088\u201396.","journal-title":"Proteins"},{"issue":"Suppl 10","key":"2017_CR30","doi-asserted-by":"publisher","first-page":"S8","DOI":"10.1186\/1471-2105-8-S10-S8","volume":"8","author":"JP Vert","year":"2007","unstructured":"Vert JP, Qiu J, Noble WS. A new pairwise kernel for biological network inference with support vector machines. BMC Bioinformatics. 2007; 8(Suppl 10):S8.","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"2017_CR31","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M Pellegrini","year":"1999","unstructured":"Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci. 1999; 96(8):4285\u20138.","journal-title":"Proc Natl Acad Sci"},{"key":"2017_CR32","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gks1239","volume":"41","author":"A Nakaya","year":"2013","unstructured":"Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 2013; 41:D353\u20137.","journal-title":"Nucleic Acids Res"},{"key":"2017_CR33","doi-asserted-by":"crossref","unstructured":"Maji S, Berg AC, Malik J. Classification using intersection kernel support vector machines is efficient. In: 2008 IEEE Conference on Computer Vision and Pattern Recognition, Anchorage, AK, p. 1\u20138. http:\/\/ieeexplore.ieee.org\/document\/4587630\/ .","DOI":"10.1109\/CVPR.2008.4587630"},{"key":"2017_CR34","doi-asserted-by":"publisher","first-page":"1458","DOI":"10.1109\/ICCV.2005.239","volume":"2","author":"K Grauman","year":"2005","unstructured":"Grauman K, Darrell T. The pyramid match kernel: Discriminative classification with sets of image features. Proc Tenth IEEE Int Conf Comput Vis. 2005; 2:1458\u201365.","journal-title":"Proc Tenth IEEE Int Conf Comput Vis"},{"key":"2017_CR35","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1109\/CVPR.2006.68","volume":"2","author":"L Lazebnik","year":"2006","unstructured":"Lazebnik L, Schmid C, Ponce J. Beyond bags of feature: Spatial pyramid matching for recognizing natural scene categories. Proc 2006 IEEE Comput Soc Conf Comput Vis Pattern Recog. 2006; 2:2169\u201378.","journal-title":"Proc 2006 IEEE Comput Soc Conf Comput Vis Pattern Recog"},{"issue":"Suppl 1","key":"2017_CR36","doi-asserted-by":"publisher","first-page":"i359","DOI":"10.1093\/bioinformatics\/bti1055","volume":"21","author":"S Swamidass","year":"2005","unstructured":"Swamidass S, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics. 2005; 21(Suppl 1):i359\u201368.","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"2017_CR37","doi-asserted-by":"publisher","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","volume":"21","author":"A Ben-Hur","year":"2005","unstructured":"Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics. 2005; 21(Suppl 1):i38\u201346.","journal-title":"Bioinformatics"},{"key":"2017_CR38","unstructured":"Osuna E, Freund R, Girosi F. Support vector machines: Training and applications. Technical Report. 1997."},{"key":"2017_CR39","volume-title":"Statistical Learning Theory","author":"V Vapnik","year":"1998","unstructured":"Vapnik V. Statistical Learning Theory. New-York: Wiley-Interscience; 1998."},{"issue":"3","key":"2017_CR40","doi-asserted-by":"publisher","first-page":"27:1","DOI":"10.1145\/1961189.1961199","volume":"2","author":"C Chang","year":"2011","unstructured":"Chang C, Lin C. A library for support vector machines. ACM Trans Intell Syst Technol. 2011; 2(3):27:1\u201327:27. http:\/\/doi.acm.org\/10.1145\/1961189.1961199 .","journal-title":"ACM Trans Intell Syst Technol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2017-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T04:09:23Z","timestamp":1693541363000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2017-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,2]]},"references-count":40,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2018,2]]}},"alternative-id":["2017"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2017-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,2]]},"assertion":[{"value":"19 February 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"39"}}