Detecting overlapping protein complexes based on a generative model with functional and topological properties

[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.