Detecting overlapping protein complexes based on a generative model with functional and topological properties
暂无分享,去创建一个
[1] Dao-Qing Dai,et al. Detecting overlapping protein complexes based on a generative model with functional and topological properties , 2014, BMC Bioinformatics.
[2] Xiaomei Quan,et al. Survey: Functional Module Detection from Protein-Protein Interaction Networks , 2014, IEEE Transactions on Knowledge and Data Engineering.
[3] A. Folkesson. IT and society , 2013 .
[4] Lusheng Wang,et al. Identifying protein complexes based on density and modularity in protein-protein interaction network , 2013, BMC Systems Biology.
[5] Hongfei Lin,et al. Construction of Ontology Augmented Networks for Protein Complex Prediction , 2013, PloS one.
[6] Keith C. C. Chan,et al. Utilizing Both Topological and Attribute Information for Protein Complex Identification in PPI Networks , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[7] Christie S. Chang,et al. The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..
[8] Hon Wai Leong,et al. A survey of computational methods for protein complex prediction from protein interaction networks , 2012, J. Bioinform. Comput. Biol..
[9] Srinivasan Parthasarathy,et al. Identifying functional modules in interaction networks through overlapping Markov clustering , 2012, Bioinform..
[10] Mario Cannataro,et al. Semantic similarity analysis of protein data: assessment with biological features and issues , 2012, Briefings Bioinform..
[11] Dao-Qing Dai,et al. Exploring Overlapping Functional Units with Various Structure in Protein Interaction Networks , 2012, PloS one.
[12] Yijia Zhang,et al. Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks , 2012, Proteome Science.
[13] Haiyuan Yu,et al. Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.
[14] 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.
[15] Alain Guénoche,et al. Multifunctional proteins revealed by overlapping clustering in protein interaction network , 2011, Bioinform..
[16] Stijn van Dongen,et al. Using MCL to extract clusters from networks. , 2012, Methods in molecular biology.
[17] M. Newman. Communities, modules and large-scale structure in networks , 2011, Nature Physics.
[18] Pavel Tomancak,et al. linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type , 2011, Bioinform..
[19] Mark E. J. Newman,et al. An efficient and principled method for detecting communities in networks , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.
[20] Kahn Rhrissorrakrai,et al. MINE: Module Identification in Networks , 2011, BMC Bioinformatics.
[21] Youping Deng,et al. Recent advances in clustering methods for protein interaction networks , 2010, BMC Genomics.
[22] Peng Jiang,et al. SPICi: a fast clustering algorithm for large biological networks , 2010, Bioinform..
[23] Xiaoli Li,et al. Computational approaches for detecting protein complexes from protein interaction networks: a survey , 2010, BMC Genomics.
[24] Sune Lehmann,et al. Link communities reveal multiscale complexity in networks , 2009, Nature.
[25] Charu C. Aggarwal,et al. Graph Clustering , 2010, Encyclopedia of Machine Learning and Data Mining.
[26] Roger Guimerà,et al. Missing and spurious interactions and the reconstruction of complex networks , 2009, Proceedings of the National Academy of Sciences.
[27] Mona Singh,et al. How and when should interactome-derived clusters be used to predict functional modules and protein function? , 2009, Bioinform..
[28] Desmond J. Higham,et al. Geometric De-noising of Protein-Protein Interaction Networks , 2009, PLoS Comput. Biol..
[29] Santo Fortunato,et al. Community detection in graphs , 2009, ArXiv.
[30] S. Pu,et al. Up-to-date catalogues of yeast protein complexes , 2008, Nucleic acids research.
[31] Sampsa Hautaniemi,et al. Fast Gene Ontology based clustering for microarray experiments , 2008, BioData Mining.
[32] C. Landry,et al. An in Vivo Map of the Yeast Protein Interactome , 2008, Science.
[33] Edoardo M. Airoldi,et al. Mixed Membership Stochastic Blockmodels , 2007, NIPS.
[34] Brad T. Sherman,et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists , 2007, Genome Biology.
[35] Aidong Zhang,et al. Semantic integration to identify overlapping functional modules in protein interaction networks , 2007, BMC Bioinformatics.
[36] T. Vicsek,et al. Weighted network modules , 2007, cond-mat/0703706.
[37] Sean R. Collins,et al. Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S , 2007, Molecular & Cellular Proteomics.
[38] Delbert Dueck,et al. Clustering by Passing Messages Between Data Points , 2007, Science.
[39] Shihua Zhang,et al. Identification of overlapping community structure in complex networks using fuzzy c-means clustering , 2007 .
[40] See-Kiong Ng,et al. Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. , 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.
[41] Zelmina Lubovac,et al. Combining functional and topological properties to identify core modules in protein interaction networks , 2006, Proteins.
[42] P. Bork,et al. Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.
[43] Sean R. Collins,et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.
[44] T. Vicsek,et al. Uncovering the overlapping community structure of complex networks in nature and society , 2005, Nature.
[45] Igor Jurisica,et al. Protein complex prediction via cost-based clustering , 2004, Bioinform..
[46] Adam J. Smith,et al. The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..
[47] L. Mirny,et al. Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[48] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.
[49] Anton J. Enright,et al. An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.
[50] Patrik O. Hoyer,et al. Non-negative sparse coding , 2002, Proceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing.
[51] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[52] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[53] H. Sebastian Seung,et al. Algorithms for Non-negative Matrix Factorization , 2000, NIPS.
[54] Dekang Lin,et al. An Information-Theoretic Definition of Similarity , 1998, ICML.
[55] David Botstein,et al. SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..
[56] David W. Conrath,et al. Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.