{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T14:33:32Z","timestamp":1768314812151,"version":"3.49.0"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"S7","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12918-017-0504-3","type":"journal-article","created":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T08:54:39Z","timestamp":1513846479000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["CPredictor3.0: detecting protein complexes from PPI networks with expression data and functional annotations"],"prefix":"10.1186","volume":"11","author":[{"given":"Ying","family":"Xu","sequence":"first","affiliation":[]},{"given":"Jiaogen","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Shuigeng","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Jihong","family":"Guan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,12,21]]},"reference":[{"issue":"7084","key":"504_CR1","doi-asserted-by":"crossref","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, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006; 440(7084):631\u20136.","journal-title":"Nature"},{"issue":"10","key":"504_CR2","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1038\/13732","volume":"17","author":"G Rigaut","year":"1999","unstructured":"Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999; 17(10):1030\u20132.","journal-title":"Nat Biotechnol"},{"issue":"2","key":"504_CR3","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai ZN. Network biology: Understanding the cell\u2019s functional organization. Nat Rev Genet. 2004; 5(2):101\u201315.","journal-title":"Nat Rev Genet"},{"key":"504_CR4","doi-asserted-by":"crossref","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":"1","key":"504_CR5","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/prot.10505","volume":"54","author":"JB Pereira-Leal","year":"2004","unstructured":"Pereira-Leal JB, Enright AJ, Ouzounis CA. Detection of functional modules from protein interaction networks. Proteins Struct Funct Bioinforma. 2004; 54(1):49\u201357.","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"5","key":"504_CR6","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nmeth.1938","volume":"9","author":"T Nepusz","year":"2012","unstructured":"Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 2012; 9(5):471\u20132.","journal-title":"Nat Methods"},{"issue":"21","key":"504_CR7","doi-asserted-by":"crossref","first-page":"12123","DOI":"10.1073\/pnas.2032324100","volume":"100","author":"V Spirin","year":"2003","unstructured":"Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci. 2003; 100(21):12123\u20138.","journal-title":"Proc Natl Acad Sci"},{"issue":"8","key":"504_CR8","doi-asserted-by":"crossref","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":"4","key":"504_CR9","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1109\/TCBB.2014.2386314","volume":"12","author":"W Zhang","year":"2015","unstructured":"Zhang W, Zou X. A new method for detecting protein complexes based on the three node cliques. IEEE\/ACM Trans Comput Biol Bioinforma. 2015; 12(4):879\u201386.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"key":"504_CR10","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1752-0509-1-8","volume":"1","author":"I Ulitsky","year":"2007","unstructured":"Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol. 2007; 1:8.","journal-title":"BMC Syst Biol"},{"issue":"6","key":"504_CR11","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1109\/TCBB.2015.2401014","volume":"12","author":"L Ou-Yang","year":"2015","unstructured":"Ou-Yang L, Dai DQ, Zhang XF. Detecting protein complexes from signed protein-protein interaction networks. IEEE\/ACM Trans Comput Biol Bioinforma. 2015; 12(6):1333\u201344.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"issue":"4","key":"504_CR12","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1002\/prot.21071","volume":"64","author":"Z Lubovac","year":"2006","unstructured":"Lubovac Z, Gamalielsson J, Olsson B. Combining functional and topological properties to identify core modules in protein interaction networks. Proteins Struct Funct Bioinforma. 2006; 64(4):948\u201359.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"504_CR13","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1471-2105-8-265","volume":"8","author":"YR Cho","year":"2007","unstructured":"Cho YR, Hwang W, Ramanathan M, Zhang A. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics. 2007; 8:265.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"504_CR14","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1089\/cmb.2008.01TT","volume":"16","author":"HCM Leung","year":"2009","unstructured":"Leung HCM, Xiang Q, Yiu SM, Chin FYL. Predicting protein complexes from ppi data: A core-attachment approach. J Comput Biol. 2009; 16(2):133\u201344.","journal-title":"J Comput Biol"},{"key":"504_CR15","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1186\/1471-2105-10-169","volume":"10","author":"M Wu","year":"2009","unstructured":"Wu M, Li X, Kwoh CK, Ng SK. A core-attachment based method to detect protein complexes in ppi networks. BMC Bioinformatics. 2009; 10:169.","journal-title":"BMC Bioinformatics"},{"key":"504_CR16","volume-title":"Lecture Notes in Bioinformatics. vol. 9683","author":"B Xu","year":"2016","unstructured":"Xu B, Guan J, Wang Y, Zhou S. Cpredictor2.0: Effectively detecting both small and large complexes from protein-protein interaction networks In: Bourgeois A, Skums P, Wan X, Zelikovsky A, editors. Lecture Notes in Bioinformatics. vol. 9683. Berlin: Springer: 2016. p. 301\u20133."},{"issue":"S12","key":"504_CR17","first-page":"19","volume":"18","author":"B Xu","year":"2017","unstructured":"Xu B, Wang Y, Wang Z, Zhou J, Zhou S, Guan J. An effective approach to detecting both small and large complexes from protein-protein interaction networks. BMC Bioinformatics. 2017; 18(S12):19\u201328.","journal-title":"BMC Bioinformatics"},{"issue":"13","key":"504_CR18","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1186\/1471-2105-12-339","volume":"12","author":"X Tang","year":"2011","unstructured":"Tang X, Wang J, Liu B, Li M, Chen G. A comparison of the functional modules identified from time course and static ppi network data. BMC Bioinformatics. 2011; 12(13):339\u201353.","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"504_CR19","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1109\/TCBB.2014.2306825","volume":"11","author":"B Xu","year":"2014","unstructured":"Xu B, Guan J. From function to interaction: A new paradigm for accurately predicting protein complexes based on protein-to-protein interaction networks. IEEE\/ACM Trans Comput Biol Bioinforma. 2014; 11(4):616\u201327.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"key":"504_CR20","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2105-7-207","volume":"7","author":"M Altaf-Ul-Amin","year":"2006","unstructured":"Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics. 2006; 7:207.","journal-title":"BMC Bioinformatics"},{"key":"504_CR21","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.compbiolchem.2015.06.006","volume":"58","author":"B Cao","year":"2015","unstructured":"Cao B, Luo J, Liang C, Wang S, Song D. Moepga: A novel method to detect protein complexes in yeast protein\u2013protein interaction networks based on multiobjective evolutionary programming genetic algorithm. Comput Biol Chem. 2015; 58:173\u201381.","journal-title":"Comput Biol Chem"},{"issue":"1","key":"504_CR22","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1109\/TCBB.2014.2343954","volume":"12","author":"W Peng","year":"2015","unstructured":"Peng W, Wang J, Zhao B, Wang L. Identification of protein complexes using weighted pagerank-nibble algorithm and core-attachment structure. IEEE\/ACM Trans Comput Biol Bioinforma (TCBB). 2015; 12(1):179\u201392.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma (TCBB)"},{"issue":"2","key":"504_CR23","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1002\/pmic.201200277","volume":"13","author":"J Wang","year":"2013","unstructured":"Wang J, Peng X, Li M, Pan Y. Construction and application of dynamic protein interaction network based on time course gene expression data. Proteomics. 2013; 13(2):301\u201312.","journal-title":"Proteomics"},{"issue":"7","key":"504_CR24","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/s12859-016-1101-y","volume":"17","author":"Y Zhang","year":"2016","unstructured":"Zhang Y, Lin H, Yang Z, Wang J, Liu Y, Sang S. A method for predicting protein complex in dynamic ppi networks. BMC Bioinformatics. 2016; 17(7):229.","journal-title":"BMC Bioinformatics"},{"key":"504_CR25","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.ins.2015.09.028","volume":"329","author":"X Lei","year":"2016","unstructured":"Lei X, Wang F, Wu FX, Zhang A, Pedrycz W. Protein complex identification through markov clustering with firefly algorithm on dynamic protein\u2013protein interaction networks. Inf Sci. 2016; 329:303\u201316.","journal-title":"Inf Sci"},{"issue":"13","key":"504_CR26","doi-asserted-by":"crossref","first-page":"250","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):250\u20138.","journal-title":"Bioinformatics"},{"issue":"S-5","key":"504_CR27","doi-asserted-by":"crossref","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(S-5):S3.","journal-title":"BMC Syst Biol"},{"issue":"Database","key":"504_CR28","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1093\/nar\/gkm936","volume":"36","author":"A Ruepp","year":"2007","unstructured":"Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, Mewes HW. Corum: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2007; 36(Database):646\u201350.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"504_CR29","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","volume":"23","author":"JZ Wang","year":"2007","unstructured":"Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of go terms. Bioinformatics. 2007; 23(10):1274\u201381.","journal-title":"Bioinformatics"},{"issue":"4","key":"504_CR30","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/s11222-007-9033-z","volume":"17","author":"U von Luxburg","year":"2007","unstructured":"von Luxburg U. A tutorial on spectral clustering. Stat Comput. 2007; 17(4):395\u2013416.","journal-title":"Stat Comput"},{"issue":"5751","key":"504_CR31","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1126\/science.1120499","volume":"310","author":"BP Tu","year":"2005","unstructured":"Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes. Science. 2005; 310(5751):1152\u20138.","journal-title":"Science"},{"issue":"7084","key":"504_CR32","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu HY, Zhong GQ, Guo XH, Ignatchenko A, Li J, Pu SY, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam M, Butland G, Altaf-Ui AM, Kanaya S, Shilatifard A, O\u2019Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature. 2006; 440(7084):637\u201343.","journal-title":"Nature"},{"issue":"3","key":"504_CR33","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1074\/mcp.M600381-MCP200","volume":"6","author":"SR Collins","year":"2007","unstructured":"Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FCP, Weissman JS, Krogan NJ. Toward a comprehensive atlas of the physical interactome of saccharomyces cerevisiae. Mol Cell Proteomics. 2007; 6(3):439\u201350.","journal-title":"Mol Cell Proteomics"},{"issue":"6","key":"504_CR34","doi-asserted-by":"crossref","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 interactome enriched for direct physical interactions. Proteomics. 2007; 7(6):932\u201343.","journal-title":"Proteomics"},{"issue":"SI","key":"504_CR35","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1093\/nar\/gkh092","volume":"32","author":"HW Mewes","year":"2004","unstructured":"Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A. Mips: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2004; 32(SI):41\u20134.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"504_CR36","doi-asserted-by":"crossref","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 SJ. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009; 37(3):825\u201331.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"504_CR37","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","volume":"26","author":"G Yu","year":"2010","unstructured":"Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. Gosemsim: an r package for measuring semantic similarity among go terms and gene products. Bioinformatics. 2010; 26(7):976\u20138.","journal-title":"Bioinformatics"},{"issue":"12","key":"504_CR38","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1186\/s12859-016-1191-6","volume":"17","author":"M Pellegrini","year":"2016","unstructured":"Pellegrini M, Baglioni M, Geraci F. Protein complex prediction for large protein protein interaction networks with the core&peel method. BMC Bioinformatics. 2016; 17(12):372.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"504_CR39","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2164-11-S1-S3","volume":"11","author":"X Li","year":"2010","unstructured":"Li X, Wu M, Kwoh CK, Ng SK. Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics. 2010; 11(1):3.","journal-title":"BMC Genomics"},{"key":"504_CR40","volume-title":"Natural Computation (ICNC), 2015 11th International Conference On","author":"J Luo","year":"2015","unstructured":"Luo J, Lin D. A cell-core-attachment approach for identifying protein complexes in ppi network. In: Natural Computation (ICNC), 2015 11th International Conference On. Piscataway: IEEE: 2015. p. 405\u201312."},{"issue":"3","key":"504_CR41","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1109\/TCBB.2013.37","volume":"10","author":"AL Hu","year":"2013","unstructured":"Hu AL, Chan KC. Utilizing both topological and attribute information for protein complex identification in ppi networks. IEEE\/ACM Trans Comput Biol Bioinforma. 2013; 10(3):780\u201392.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinforma"},{"issue":"2","key":"504_CR42","first-page":"260","volume":"16","author":"XL Li","year":"2005","unstructured":"Li XL, Foo CS, Tan SH, Ng SK. Interaction graph mining for protein complexes using local clique merging. Genome Inform. 2005; 16(2):260\u20139.","journal-title":"Genome Inform"},{"issue":"Suppl 6","key":"504_CR43","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1752-0509-7-S6-S14","volume":"7","author":"CK Widita","year":"2013","unstructured":"Widita CK, Maruyama O. Ppsampler2: Predicting protein complexes more accurately and efficiently by sampling. BMC Syst Biol. 2013; 7(Suppl 6):14.","journal-title":"BMC Syst Biol"},{"issue":"17","key":"504_CR44","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.1093\/bioinformatics\/bth351","volume":"20","author":"AD King","year":"2004","unstructured":"King AD, Przulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics. 2004; 20(17):3013\u201320.","journal-title":"Bioinformatics"},{"key":"504_CR45","volume-title":"Proceedings of AAAI","author":"L Gao","year":"2016","unstructured":"Gao L, Zhou S. Group and graph joint sparsity for linked data classification In: Schuurmans D, Wellman MP, editors. Proceedings of AAAI. Palo Alto: AAAI press: 2016."},{"key":"504_CR46","volume-title":"Proceedings of KDD","author":"Y Yang","year":"2016","unstructured":"Yang Y, Yan D, Wu H, Cheng J, Zhou S, Lui JCS. Diversified temporal subgraph pattern mining In: Krishnapuram B, Shah M, Smola AJ, Aggarwal CC, Shen D, Rastogi R, editors. Proceedings of KDD. New York: ACM: 2016."},{"issue":"S12","key":"504_CR47","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12859-017-1819-1","volume":"18","author":"X Zheng","year":"2017","unstructured":"Zheng X, Wang Y, Tian K, Zhou J, Guan J, Luo L, Zhou S. Fusing multiple protein-protein similarity networks to effectively predict lncrna-protein interactions. BMC Bioinformatics. 2017; 18(S12):11\u201318.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-017-0504-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T08:55:50Z","timestamp":1513846550000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-017-0504-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":47,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["504"],"URL":"https:\/\/doi.org\/10.1186\/s12918-017-0504-3","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12]]},"article-number":"135"}}