Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization
暂无分享,去创建一个
[1] Kara Dolinski,et al. Gene Ontology annotations at SGD: new data sources and annotation methods , 2007, Nucleic Acids Res..
[2] Illés J. Farkas,et al. CFinder: locating cliques and overlapping modules in biological networks , 2006, Bioinform..
[3] B. Schwikowski,et al. A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.
[4] B. Séraphin,et al. A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.
[5] Mike Tyers,et al. BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..
[6] H. Sebastian Seung,et al. Algorithms for Non-negative Matrix Factorization , 2000, NIPS.
[7] Santo Fortunato,et al. Consensus clustering in complex networks , 2012, Scientific Reports.
[8] Joydeep Ghosh,et al. Cluster Ensembles --- A Knowledge Reuse Framework for Combining Multiple Partitions , 2002, J. Mach. Learn. Res..
[9] Srinivasan Parthasarathy,et al. An ensemble framework for clustering protein-protein interaction networks , 2007, ISMB/ECCB.
[10] Xiaoli Li,et al. Computational approaches for detecting protein complexes from protein interaction networks: a survey , 2010, BMC Genomics.
[11] Gary D Bader,et al. A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.
[12] Youping Deng,et al. Recent advances in clustering methods for protein interaction networks , 2010, BMC Genomics.
[13] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.
[14] David Botstein,et al. SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..
[15] Xian-Sheng Hua,et al. Ensemble Manifold Regularization , 2009, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[16] Dao-Qing Dai,et al. Exploring Overlapping Functional Units with Various Structure in Protein Interaction Networks , 2012, PloS one.
[17] Derek Greene,et al. Ensemble non-negative matrix factorization methods for clustering protein-protein interactions , 2008, Bioinform..
[18] H. Sebastian Seung,et al. Learning the parts of objects by non-negative matrix factorization , 1999, Nature.
[19] Mona Singh,et al. How and when should interactome-derived clusters be used to predict functional modules and protein function? , 2009, Bioinform..
[20] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[21] Dao-Qing Dai,et al. A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[22] David Mackay,et al. Probable networks and plausible predictions - a review of practical Bayesian methods for supervised neural networks , 1995 .
[23] Michael K. Ng,et al. Agglomerative Fuzzy K-Means Clustering Algorithm with Selection of Number of Clusters , 2008, IEEE Transactions on Knowledge and Data Engineering.
[24] Gary D Bader,et al. Analyzing yeast protein–protein interaction data obtained from different sources , 2002, Nature Biotechnology.
[25] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[26] Steve Gregory,et al. Finding overlapping communities in networks by label propagation , 2009, ArXiv.
[27] Shigehiko Kanaya,et al. Development and implementation of an algorithm for detection of protein complexes in large interaction networks , 2006, BMC Bioinformatics.
[28] Ioannis Psorakis,et al. Soft Partitioning in Networks via Bayesian Non-negative Matrix Factorization , 2010 .
[29] Kara Dolinski,et al. The BioGRID Interaction Database: 2011 update , 2010, Nucleic Acids Res..
[30] Dao-Qing Dai,et al. Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[31] Michael L. Creech,et al. Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.
[32] Dmitrij Frishman,et al. MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2006, Nucleic Acids Res..
[33] C. Févotte,et al. Automatic Relevance Determination in Nonnegative Matrix Factorization , 2009 .
[34] C. Landry,et al. An in Vivo Map of the Yeast Protein Interactome , 2008, Science.
[35] Peng Jiang,et al. SPICi: a fast clustering algorithm for large biological networks , 2010, Bioinform..
[36] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[37] M E J Newman,et al. Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[38] Igor Jurisica,et al. Protein complex prediction via cost-based clustering , 2004, Bioinform..
[39] Sean R. Collins,et al. Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S , 2007, Molecular & Cellular Proteomics.
[40] Aidong Zhang,et al. Semantic integration to identify overlapping functional modules in protein interaction networks , 2007, BMC Bioinformatics.
[41] Réka Albert,et al. Near linear time algorithm to detect community structures in large-scale networks. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.
[42] Roded Sharan,et al. Associating Genes and Protein Complexes with Disease via Network Propagation , 2010, PLoS Comput. Biol..
[43] T. Vicsek,et al. Uncovering the overlapping community structure of complex networks in nature and society , 2005, Nature.
[44] C. Févotte,et al. Automatic Relevance Determination in Nonnegative Matrix Factorization with the-Divergence , 2011 .
[45] Sean R. Collins,et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.
[46] P. Bork,et al. Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.
[47] Sune Lehmann,et al. Link communities reveal multiscale complexity in networks , 2009, Nature.
[48] Xiaomei Quan,et al. Survey: Functional Module Detection from Protein-Protein Interaction Networks , 2014, IEEE Transactions on Knowledge and Data Engineering.
[49] Anil K. Jain,et al. Clustering ensembles: models of consensus and weak partitions , 2005, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[50] Hyunsoo Kim,et al. Sparse Non-negative Matrix Factorizations via Alternating Non-negativity-constrained Least Squares , 2006 .
[51] Kahn Rhrissorrakrai,et al. MINE: Module Identification in Networks , 2011, BMC Bioinformatics.
[52] R. Ozawa,et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[53] Anton J. Enright,et al. An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.
[54] Jacques van Helden,et al. Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.
[55] Alain Guénoche,et al. Multifunctional proteins revealed by overlapping clustering in protein interaction network , 2011, Bioinform..
[56] Yanjun Qi,et al. Protein complex identification by supervised graph local clustering , 2008, ISMB.
[57] Guimei Liu,et al. Complex discovery from weighted PPI networks , 2009, Bioinform..
[58] Haiyuan Yu,et al. Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.
[59] A. Barabasi,et al. Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.