{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T19:53:47Z","timestamp":1760385227375},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"S7","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. However, these high-throughput protein interaction data are often associated with high false positive and false negative rates. It is therefore highly desirable to develop scalable methods to identify these errors from the computational perspective.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed a robust computational technique for assessing the reliability of interactions and predicting new interactions by combining manifold embedding with multiple information integration. Validation of the proposed method was performed with extensive experiments on densely-connected and sparse PPI networks of yeast respectively. Results demonstrate that the interactions ranked top by our method have high functional homogeneity and localization coherence.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our proposed method achieves better performances than the existing methods no matter assessing or predicting protein interactions. Furthermore, our method is general enough to work over a variety of PPI networks irrespectively of densely-connected or sparse PPI network. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions in PPI networks.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-s7-s3","type":"journal-article","created":{"date-parts":[[2012,5,8]],"date-time":"2012-05-08T12:31:53Z","timestamp":1336480313000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Assessing and predicting protein interactions by combining manifold embedding with multiple information integration"],"prefix":"10.1186","volume":"13","author":[{"given":"Ying-Ke","family":"Lei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhu-Hong","family":"You","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Ji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"De-Shuang","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,5,8]]},"reference":[{"key":"5156_CR1","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1016\/j.drudis.2008.05.004","volume":"13","author":"HN Chua","year":"2008","unstructured":"Chua HN, Wong L: Increasing the reliability of protein interactomes. Drug Discov Today 2008, 13: 652\u2013658. 10.1016\/j.drudis.2008.05.004","journal-title":"Drug Discov Today"},{"issue":"10","key":"5156_CR2","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/S0168-9525(02)02763-4","volume":"18","author":"AM Edwards","year":"2002","unstructured":"Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M: Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet 2002, 18(10):529\u2013536. 10.1016\/S0168-9525(02)02763-4","journal-title":"Trends Genet"},{"issue":"5","key":"5156_CR3","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1093\/nar\/30.5.1163","volume":"30","author":"R Saito","year":"2002","unstructured":"Saito R, Suzuki H, Hayashizaki Y: Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Res 2002, 30(5):1163\u20131168. 10.1093\/nar\/30.5.1163","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"5156_CR4","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1093\/bioinformatics\/btg070","volume":"19","author":"R Saito","year":"2003","unstructured":"Saito R, Suzuki H, Hayashizaki Y: Construction of reliable protein-protein interaction networks with a new interaction generality measure. Bioinformatics 2003, 19(6):756\u2013763. 10.1093\/bioinformatics\/btg070","journal-title":"Bioinformatics"},{"key":"5156_CR5","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.artmed.2005.02.004","volume":"35","author":"J Chen","year":"2005","unstructured":"Chen J, Hsu W, Lee ML, Ng S-K: Discovering reliable protein interactions from high-throughput experimental data using network topology. Artif Intell Med 2005, 35: 37\u201347. 10.1016\/j.artmed.2005.02.004","journal-title":"Artif Intell Med"},{"issue":"16","key":"5156_CR6","doi-asserted-by":"publisher","first-page":"1998","DOI":"10.1093\/bioinformatics\/btl335","volume":"22","author":"J Chen","year":"2006","unstructured":"Chen J, Hsu W, Lee ML, Ng S-K: Increasing confidence of protein interactomes using network topological metrics. Bioinformatics 2006, 22(16):1998\u20132004. 10.1093\/bioinformatics\/btl335","journal-title":"Bioinformatics"},{"issue":"1","key":"5156_CR7","doi-asserted-by":"publisher","first-page":"R6","DOI":"10.1186\/gb-2003-5-1-r6","volume":"5","author":"C Brun","year":"2003","unstructured":"Brun C, Chevent F, Martin D, Wojcik J, Guenoche A, Jacq B: Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 2003, 5(1):R6. 10.1186\/gb-2003-5-1-r6","journal-title":"Genome Biol"},{"issue":"13","key":"5156_CR8","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1093\/bioinformatics\/btl145","volume":"22","author":"HN Chua","year":"2006","unstructured":"Chua HN, Sung WK, Wong L: Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22(13):1623\u20131630. 10.1093\/bioinformatics\/btl145","journal-title":"Bioinformatics"},{"issue":"1","key":"5156_CR9","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/nbt924","volume":"22","author":"JS Bader","year":"2004","unstructured":"Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22(1):78\u201385. 10.1038\/nbt924","journal-title":"Nat Biotechnol"},{"issue":"5644","key":"5156_CR10","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1126\/science.1087361","volume":"302","author":"R Jansen","year":"2003","unstructured":"Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, et al.: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302(5644):449\u2013453. 10.1126\/science.1087361","journal-title":"Science"},{"issue":"1","key":"5156_CR11","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1101\/gr.205602","volume":"12","author":"R Jansen","year":"2002","unstructured":"Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12(1):37\u201346. 10.1101\/gr.205602","journal-title":"Genome Res"},{"key":"5156_CR12","first-page":"531","volume":"10","author":"Y Qi","year":"2005","unstructured":"Qi Y, Klien-Seetharaman J, Bar-Joseph Z: Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput 2005, 10: 531\u2013542.","journal-title":"Pac Symp Biocomput"},{"key":"5156_CR13","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1109\/BIBE.2004.1317394","volume-title":"Proc Fourth IEEE Symposium on Bioinformatics and Bioengineering","author":"S Dohkan","year":"2004","unstructured":"Dohkan S, Koike A, Takagi T: Prediction of protein-protein interactions using support vector machines. Proc Fourth IEEE Symposium on Bioinformatics and Bioengineering 2004, 576\u2013583."},{"issue":"2","key":"5156_CR14","doi-asserted-by":"publisher","first-page":"e177","DOI":"10.1093\/bioinformatics\/btl301","volume":"23","author":"N Przulj","year":"2006","unstructured":"Przulj N: Biological network comparison using graphlet degree distribution. Bioinformatics 2006, 23(2):e177-e183.","journal-title":"Bioinformatics"},{"issue":"10","key":"5156_CR15","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1098\/rsif.2006.0147","volume":"3","author":"N Przulj","year":"2006","unstructured":"Przulj N, Higham D: Modelling protein-protein interaction networks via stickiness index. J R Soc Interface 2006, 3(10):711\u2013716. 10.1098\/rsif.2006.0147","journal-title":"J R Soc Interface"},{"issue":"18","key":"5156_CR16","doi-asserted-by":"publisher","first-page":"3508","DOI":"10.1093\/bioinformatics\/bth436","volume":"20","author":"N Przulj","year":"2004","unstructured":"Przulj N, Corneil DG, Jurisica I: Modeling interactome: scale-free or geometric? Bioinformatics 2004, 20(18):3508\u20133515. 10.1093\/bioinformatics\/bth436","journal-title":"Bioinformatics"},{"issue":"8","key":"5156_CR17","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1093\/bioinformatics\/btl030","volume":"22","author":"N Przulj","year":"2006","unstructured":"Przulj N, Corneil DG, Jurisica I: Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics 2006, 22(8):974\u2013980. 10.1093\/bioinformatics\/btl030","journal-title":"Bioinformatics"},{"issue":"8","key":"5156_CR18","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1093\/bioinformatics\/btn079","volume":"24","author":"DJ Higham","year":"2008","unstructured":"Higham DJ, Rasajski M, Przulj N: Fitting a geometric graph to a protein-protein interaction network. Bioinformatics 2008, 24(8):1093\u20131099. 10.1093\/bioinformatics\/btn079","journal-title":"Bioinformatics"},{"issue":"8","key":"5156_CR19","doi-asserted-by":"publisher","first-page":"e1000454","DOI":"10.1371\/journal.pcbi.1000454","volume":"5","author":"O Kuchaiev","year":"2009","unstructured":"Kuchaiev O, Rasajski M, Higham DJ, Przulj N: Geometric de-noising of protein-protein interaction networks. PLoS Comput Biol 2009, 5(8):e1000454. 10.1371\/journal.pcbi.1000454","journal-title":"PLoS Comput Biol"},{"key":"5156_CR20","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1074\/mcp.M400048-MCP200","volume":"3","author":"L Terradot","year":"2004","unstructured":"Terradot L, Durnell N, Li M, Ory J, Labigne A, Legrain P, Colland F, Waksman G: Biochemical characterization of protein complexes from the helicobacter pylori protein interaction map: strategies for complex formation and evidence for novel interactions within type IV secretion systems. Mol Cell Proteomics 2004, 3: 809\u2013819. 10.1074\/mcp.M400048-MCP200","journal-title":"Mol Cell Proteomics"},{"key":"5156_CR21","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1126\/science.290.5500.2319","volume":"290","author":"J Tenenbaum","year":"2000","unstructured":"Tenenbaum J, de Silva V, Langford J: A global geometric framework for nonlinear dimensionality reduction. Science 2000, 290: 2319\u20132323. 10.1126\/science.290.5500.2319","journal-title":"Science"},{"key":"5156_CR22","doi-asserted-by":"publisher","first-page":"2323","DOI":"10.1126\/science.290.5500.2323","volume":"290","author":"S Roweis","year":"2000","unstructured":"Roweis S, Saul L: Nonlinear dimensionality reduction by locally linear embedding. Science 2000, 290: 2323\u20132326. 10.1126\/science.290.5500.2323","journal-title":"Science"},{"key":"5156_CR23","first-page":"119","volume":"4","author":"LK Saul","year":"2003","unstructured":"Saul LK, Roweis ST: Think globally, fit locally: unsupervised learning of low dimensional manifold. J Machine Learning Research 2003, 4: 119\u2013155.","journal-title":"J Machine Learning Research"},{"issue":"6","key":"5156_CR24","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1162\/089976603321780317","volume":"15","author":"M Belkin","year":"2003","unstructured":"Belkin M, Niyogi P: Laplacian eigenmaps for dimensionality reduction and data representation. Neural Comput 2003, 15(6):1373\u20131396. 10.1162\/089976603321780317","journal-title":"Neural Comput"},{"issue":"10","key":"5156_CR25","doi-asserted-by":"publisher","first-page":"5591","DOI":"10.1073\/pnas.1031596100","volume":"100","author":"D Donoho","year":"2003","unstructured":"Donoho D, Grimes C: Hessian eigenmaps: new locally linear embedding techniques for high-dimensional data. Proc Natl Acad Sci USA 2003, 100(10):5591\u20135596. 10.1073\/pnas.1031596100","journal-title":"Proc Natl Acad Sci USA"},{"key":"5156_CR26","first-page":"988","volume":"2","author":"K Weinberger","year":"2004","unstructured":"Weinberger K, Saul L: Unsupervised learning of image manifolds by semidefinite programming. Proc IEEE Intl Conf Computer Vision and Pattern Recognition 2004, 2: 988\u2013995.","journal-title":"Proc IEEE Intl Conf Computer Vision and Pattern Recognition"},{"key":"5156_CR27","first-page":"961","volume":"15","author":"M Brand","year":"2003","unstructured":"Brand M: Charting a manifold. Proc Advances in Neural Information Processing Systems 2003, 15: 961\u2013968.","journal-title":"Proc Advances in Neural Information Processing Systems"},{"issue":"1","key":"5156_CR28","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1137\/S1064827502419154","volume":"26","author":"Z Zhang","year":"2005","unstructured":"Zhang Z, Zha H: Principal manifolds and nonlinear dimension reduction via local tangent space alignment. SIAM J Scientific Computing 2005, 26(1):313\u2013338.","journal-title":"SIAM J Scientific Computing"},{"key":"5156_CR29","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/j.acha.2006.04.006","volume":"21","author":"RR Coifman","year":"2006","unstructured":"Coifman RR, Lafon S: Diffusion maps. Appl Comput Harmon Anal 2006, 21: 5\u201330. 10.1016\/j.acha.2006.04.006","journal-title":"Appl Comput Harmon Anal"},{"issue":"9","key":"5156_CR30","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1109\/TPAMI.2006.184","volume":"28","author":"S Lafon","year":"2006","unstructured":"Lafon S, Lee AB: Diffusion maps and coarse-graining: a unified framework for dimensionality reduction, graph partitioning and data set parameterization. IEEE Trans Pattern Anal Mach Intell 2006, 28(9):1393\u20131403.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"5156_CR31","first-page":"44","volume-title":"Proc Ninth European Conf Computer Vision","author":"T Lin","year":"2006","unstructured":"Lin T, Zha H, Lee S: Riemannian manifold learning for nonlinear dimensionality reduction. Proc Ninth European Conf Computer Vision 2006, 44\u201355."},{"issue":"5","key":"5156_CR32","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1109\/TPAMI.2007.70735","volume":"30","author":"T Lin","year":"2008","unstructured":"Lin T, Zha HB: Riemannian manifold learning. IEEE Trans Pattern Anal Mach Intell 2008, 30(5):796\u2013809.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"9","key":"5156_CR33","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1109\/TKDE.2008.204","volume":"21","author":"SM Xiang","year":"2009","unstructured":"Xiang SM, Nie FP, Zhang CS: Nonlinear dimensionality reduction with local spline embedding. IEEE Trans Knowledge and Data Engineering 2009, 21(9):1285\u20131298.","journal-title":"IEEE Trans Knowledge and Data Engineering"},{"issue":"1","key":"5156_CR34","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/nar\/28.1.289","volume":"28","author":"I Xenarios","year":"2000","unstructured":"Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D: DIP: the database of interacting proteins. Nucleic Acids Res 2000, 28(1):289\u2013291. 10.1093\/nar\/28.1.289","journal-title":"Nucleic Acids Res"},{"key":"5156_CR35","doi-asserted-by":"publisher","first-page":"D637","DOI":"10.1093\/nar\/gkm1001","volume":"36","author":"BJ Breitkreutz","year":"2008","unstructured":"Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, et al.: The BioGRID interaction database: 2008 update. Nucleic Acids Res 2008, 36: D637-D640.","journal-title":"Nucleic Acids Res"},{"issue":"7084","key":"5156_CR36","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, Ignatchenko A, et al.: Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature 2006, 440(7084):637\u2013643. 10.1038\/nature04670","journal-title":"Nature"},{"issue":"7084","key":"5156_CR37","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, Marzioch M, et al.: Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440(7084):631\u2013636. 10.1038\/nature04532","journal-title":"Nature"},{"key":"5156_CR38","doi-asserted-by":"publisher","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: 439\u2013450.","journal-title":"Mol Cell Proteomics"},{"issue":"5659","key":"5156_CR39","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1126\/science.1091317","volume":"303","author":"AHY Tong","year":"2004","unstructured":"Tong AHY, Lesage G, Bader GD, Ding HM, Xu H, Xin XF, et al.: Global mapping of the yeast genetic interaction network. Science 2004, 303(5659):808\u2013813. 10.1126\/science.1091317","journal-title":"Science"},{"key":"5156_CR40","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1038\/35001165","volume":"403","author":"S Oliver","year":"2000","unstructured":"Oliver S: Guilt-by-association goes global. Nature 2000, 403: 601\u2013603. 10.1038\/35001165","journal-title":"Nature"},{"key":"5156_CR41","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1101\/gr.180801","volume":"11","author":"The Gene Ontology Consortium","year":"2001","unstructured":"The Gene Ontology Consortium: Creating the gene ontology resource: design and implementation. Genome Res 2001, 11: 1425\u20131433. 10.1101\/gr.180801","journal-title":"Genome Res"},{"key":"5156_CR42","first-page":"178","volume-title":"Pac Symp Biocomput","author":"R Colak","year":"2009","unstructured":"Colak R, Hormozdiari F, Moser F, Schonhuth A, Holman J, Ester M, Sahinalp SC: Dense graphlet statistics of protein interaction and random networks. Pac Symp Biocomput 2009, 178\u2013189."},{"key":"5156_CR43","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1007\/s11390-010-9310-8","volume":"25","author":"LS Wong","year":"2010","unstructured":"Wong LS, Liu GM: Protein interactome analysis for countering pathogen drug resistance. J Comput Sci Technol 2010, 25: 124\u2013130. 10.1007\/s11390-010-9310-8","journal-title":"J Comput Sci Technol"},{"key":"5156_CR44","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1002\/prot.20865","volume":"63","author":"Y Qi","year":"2006","unstructured":"Qi Y, Klien-Seetharaman J, Bar-Joseph Z: Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 2006, 63: 490\u2013500. 10.1002\/prot.20865","journal-title":"Proteins"},{"key":"5156_CR45","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-8-S10-S6","volume":"8","author":"Y Qi","year":"2007","unstructured":"Qi Y, Klien-Seetharaman J, Bar-Joseph Z: A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics 2007, 8: S6.","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"5156_CR46","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/nbt890","volume":"21","author":"Z Bar-Joseph","year":"2003","unstructured":"Bar-Joseph Z, Gerber G, Lee T, Rinaldi N, Yoo J, Robert F, Gordon B, Fraenkel E, Jaakkola T, Young R, Gifford D: Computational discovery of gene modules and regulatory networks. Nat Biotechnol 2003, 21(11):1337\u20131342. 10.1038\/nbt890","journal-title":"Nat Biotechnol"},{"key":"5156_CR47","unstructured":"The Saccharomyces Genome Deletion Project[http:\/\/www-sequence.stanford.edu\/group\/yeast_deletion_project] (2004 Nov version)"},{"issue":"7004","key":"5156_CR48","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature02800","volume":"431","author":"CT Harbison","year":"2004","unstructured":"Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, et al.: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431(7004):99\u2013104. 10.1038\/nature02800","journal-title":"Nature"},{"issue":"10","key":"5156_CR49","doi-asserted-by":"publisher","first-page":"1540","DOI":"10.1101\/gr.153002","volume":"12","author":"M Deng","year":"2002","unstructured":"Deng M, Mehta S, Sun F, Chen T: Inferring domain-domain interactions from protein-protein interactions. Genome Res 2002, 12(10):1540\u20138. 10.1101\/gr.153002","journal-title":"Genome Res"},{"key":"5156_CR50","volume-title":"Saccharomyces genome database (SGD)","author":"K Dolinski","year":"2004","unstructured":"Dolinski K, Balakrishnan R, Christie KR, Costanzo MC: Saccharomyces genome database (SGD).2004. [http:\/\/www.yeastgenome.org]"},{"key":"5156_CR51","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1186\/1471-2105-5-154","volume":"5","author":"N Lin","year":"2004","unstructured":"Lin N, Wu B, Jansen R, Gerstein M, Zhao H: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004, 5: 154. 10.1186\/1471-2105-5-154","journal-title":"BMC Bioinformatics"},{"key":"5156_CR52","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/1471-2105-8-239","volume":"8","author":"MS Scott","year":"2007","unstructured":"Scott MS, Barton GJ: Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics 2007, 8: 239. 10.1186\/1471-2105-8-239","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"5156_CR53","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/bioinformatics\/btn592","volume":"25","author":"MA Sartor","year":"2009","unstructured":"Sartor MA, Leikauf GD, Medvedovic M: LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics 2009, 25(2):211\u2013217. 10.1093\/bioinformatics\/btn592","journal-title":"Bioinformatics"},{"key":"5156_CR54","doi-asserted-by":"publisher","first-page":"2744","DOI":"10.1093\/bioinformatics\/btq510","volume":"26","author":"ZH You","year":"2010","unstructured":"You ZH, Lei YK, Huang DS, Zhou XB: Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. Bioinformatics 2010, 26: 2744\u20132751. 10.1093\/bioinformatics\/btq510","journal-title":"Bioinformatics"},{"key":"5156_CR55","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF02288320","volume":"13","author":"G Gall","year":"1988","unstructured":"Gall G, Pallottino S: Shortest path algorithms. Annals of Operations Research 1988, 13: 1\u201379. 10.1007\/BF02288320","journal-title":"Annals of Operations Research"},{"key":"5156_CR56","volume-title":"Graph approximations to geodesics on embedded manifolds","author":"M Bernstein","year":"2000","unstructured":"Bernstein M, de Silva V, Langford JC, Tenenbaum JB: Graph approximations to geodesics on embedded manifolds. Stanford University, Department of Psychology; 2000."},{"key":"5156_CR57","volume-title":"Multidimensional Scaling","author":"TF Cox","year":"1994","unstructured":"Cox TF, Cox MAA: Multidimensional Scaling. London: Chapman & Hall; 1994."},{"key":"5156_CR58","first-page":"705","volume":"15","author":"V de Silva","year":"2003","unstructured":"de Silva V, Tenenbaum JB: Global versus local methods in nonlinear dimensionality reduction. Proc of NIPS 2003, 15: 705\u2013712.","journal-title":"Proc of NIPS"},{"key":"5156_CR59","volume-title":"Computers and Intractability: A Guide to the Theory of NP-Completeness","author":"MR Garey","year":"1979","unstructured":"Garey MR, Johnson DS: Computers and Intractability: A Guide to the Theory of NP-Completeness. WH Freeman; 1979."},{"key":"5156_CR60","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/978-1-4684-2001-2_9","volume-title":"Complexity of Computer Computations","author":"RM Karp","year":"1972","unstructured":"Karp RM: Reducibility among combinatorial problems. In Complexity of Computer Computations. Edited by: Miller RE, Thatcher JW. Plenum Press; 1972:85\u2013103."},{"key":"5156_CR61","volume-title":"Technical report","author":"V de Silva","year":"2004","unstructured":"de Silva V, Tenenbaum J: Sparse multidimensional scaling using landmark points. In Technical report. Stanford University; 2004."},{"key":"5156_CR62","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s11634-008-0018-3","volume":"2","author":"JB Angelelli","year":"2008","unstructured":"Angelelli JB, Baudot A, Brun C, Guenoche A: Two local dissimilarity measures for weighted graphs with application to protein interaction networks. Adv Data Anal Classif 2008, 2: 3\u201316. 10.1007\/s11634-008-0018-3","journal-title":"Adv Data Anal Classif"},{"issue":"2","key":"5156_CR63","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/j.febslet.2005.11.081","volume":"580","author":"B Wang","year":"2006","unstructured":"Wang B, Chen P, Huang DS, Li J-J, Lok T-M, Lyu MR: Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 2006, 580(2):380\u2013384. 10.1016\/j.febslet.2005.11.081","journal-title":"FEBS Lett"},{"issue":"10","key":"5156_CR64","doi-asserted-by":"publisher","first-page":"999","DOI":"10.2174\/092986606778777498","volume":"13","author":"B Wang","year":"2006","unstructured":"Wang B, Wong HS, Huang DS: Inferring protein-protein interaction sites from residue evolutionary conservation information. Protein Pept Lett 2006, 13(10):999\u20131005. 10.2174\/092986606778777498","journal-title":"Protein Pept Lett"},{"issue":"9","key":"5156_CR65","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.2174\/092986610791760397","volume":"17","author":"B Wang","year":"2010","unstructured":"Wang B, Chen P, Wang PZ, Zhao GX, Zhang X: Radial basis function neural network ensemble for predicting protein-protein interaction sites in heterocomplexes. Protein Pept Lett 2010, 17(9):1111\u20131116. 10.2174\/092986610791760397","journal-title":"Protein Pept Lett"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S7-S3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T19:00:58Z","timestamp":1630522858000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S7-S3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,8]]},"references-count":65,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5156"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s7-s3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,5,8]]},"assertion":[{"value":"8 May 2012","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S3"}}