Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks
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Ru Shen | Chittibabu Guda | C. Guda | Ru Shen
[1] Sune Lehmann,et al. Link communities reveal multiscale complexity in networks , 2009, Nature.
[2] Chris H. Q. Ding,et al. Determining modular organization of protein interaction networks by maximizing modularity density , 2010, BMC Systems Biology.
[3] Kaushal K. Shukla,et al. COMPARATIVE PERFORMANCE ANALYSIS OF RNSC AND MCL ALGORITHMS ON POWER-LAW DISTRIBUTION , 2012 .
[4] Jan Ramon,et al. Expressivity versus efficiency of graph kernels , 2003 .
[5] Hans-Peter Kriegel,et al. Protein function prediction via graph kernels , 2005, ISMB.
[6] D. Bu,et al. the protein–protein interaction network , 2004 .
[7] Fred W. Glover,et al. Tabu Search - Part I , 1989, INFORMS J. Comput..
[8] David Martin,et al. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network , 2003, Genome Biology.
[9] Natasa Przulj,et al. Integrative network alignment reveals large regions of global network similarity in yeast and human , 2011, Bioinform..
[10] M. Porter,et al. Critical Truths About Power Laws , 2012, Science.
[11] R. Karp,et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[12] Roded Sharan,et al. Fast and Accurate Alignment of Multiple Protein Networks , 2009, J. Comput. Biol..
[13] Benno Schwikowski,et al. Discovering regulatory and signalling circuits in molecular interaction networks , 2002, ISMB.
[14] Frans Coenen,et al. A survey of frequent subgraph mining algorithms , 2012, The Knowledge Engineering Review.
[15] Wojciech Szpankowski,et al. Pairwise Alignment of Protein Interaction Networks , 2006, J. Comput. Biol..
[16] Vasant Honavar,et al. Aligning Biomolecular Networks Using Modular Graph Kernels , 2009, WABI.
[17] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[18] Yanjun Qi,et al. Protein complex identification by supervised graph local clustering , 2008, ISMB.
[19] Anastasios Bezerianos,et al. Growing functional modules from a seed protein via integration of protein interaction and gene expression data , 2007, BMC Bioinformatics.
[20] Kurt Mehlhorn,et al. Efficient graphlet kernels for large graph comparison , 2009, AISTATS.
[21] L. R. Dice. Measures of the Amount of Ecologic Association Between Species , 1945 .
[22] Behnam Neyshabur,et al. NETAL: a new graph-based method for global alignment of protein-protein interaction networks , 2013, Bioinform..
[23] Serafim Batzoglou,et al. Automatic Parameter Learning for Multiple Local Network Alignment , 2009, J. Comput. Biol..
[24] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[25] Igor Jurisica,et al. Protein complex prediction via cost-based clustering , 2004, Bioinform..
[26] George Karypis,et al. An efficient algorithm for discovering frequent subgraphs , 2004, IEEE Transactions on Knowledge and Data Engineering.
[27] Kurt Mehlhorn,et al. Weisfeiler-Lehman Graph Kernels , 2011, J. Mach. Learn. Res..
[28] Antal F. Novak,et al. networks Græmlin : General and robust alignment of multiple large interaction data , 2006 .
[29] M E J Newman,et al. Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[30] Xiujuan Lei,et al. Protein complex detection with semi-supervised learning in protein interaction networks , 2011, Proteome Science.
[31] A. Barabasi,et al. Lethality and centrality in protein networks , 2001, Nature.
[32] King-Sun Fu,et al. A distance measure between attributed relational graphs for pattern recognition , 1983, IEEE Transactions on Systems, Man, and Cybernetics.
[33] Wayne Hayes,et al. Optimal Network Alignment with Graphlet Degree Vectors , 2010, Cancer informatics.
[34] Robert Patro,et al. Global network alignment using multiscale spectral signatures , 2012, Bioinform..
[35] Tijana Milenkovic,et al. Graphlet-based edge clustering reveals pathogen-interacting proteins , 2012, Bioinform..
[36] Hans-Peter Kriegel,et al. Shortest-path kernels on graphs , 2005, Fifth IEEE International Conference on Data Mining (ICDM'05).
[37] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.
[38] Ru Shen,et al. Mining functional subgraphs from cancer protein-protein interaction networks , 2012, BMC Systems Biology.
[39] Peng Jiang,et al. SPICi: a fast clustering algorithm for large biological networks , 2010, Bioinform..
[40] Roded Sharan,et al. PathBLAST: a tool for alignment of protein interaction networks , 2004, Nucleic Acids Res..
[41] Horst Bunke,et al. A graph distance metric based on the maximal common subgraph , 1998, Pattern Recognit. Lett..
[42] Bonnie Berger,et al. Global alignment of multiple protein interaction networks with application to functional orthology detection , 2008, Proceedings of the National Academy of Sciences.
[43] Hisashi Kashima,et al. Marginalized Kernels Between Labeled Graphs , 2003, ICML.
[44] David Haussler,et al. Convolution kernels on discrete structures , 1999 .
[45] Jiawei Han,et al. gSpan: graph-based substructure pattern mining , 2002, 2002 IEEE International Conference on Data Mining, 2002. Proceedings..
[46] Gabriel Valiente,et al. A graph distance metric combining maximum common subgraph and minimum common supergraph , 2001, Pattern Recognit. Lett..
[47] Karsten M. Borgwardt,et al. Fast subtree kernels on graphs , 2009, NIPS.
[48] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[49] Yong Wang,et al. Alignment of Protein Interaction Networks by Integer Quadratic Programming , 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.
[50] Fred Glover,et al. Tabu Search - Part II , 1989, INFORMS J. Comput..
[51] Bonnie Berger,et al. IsoRankN: spectral methods for global alignment of multiple protein networks , 2009, Bioinform..
[52] B MolerCleve,et al. Solution of the Sylvester matrix equation AXBT + CXDT = E , 1992 .
[53] S. Dongen. Graph clustering by flow simulation , 2000 .
[54] D K Smith,et al. Numerical Optimization , 2001, J. Oper. Res. Soc..
[55] Vesna Memisevic,et al. Global G RAph A Lignment of Biological Networks , 2022 .
[56] Thomas Gärtner,et al. On Graph Kernels: Hardness Results and Efficient Alternatives , 2003, COLT.
[57] Roded Sharan,et al. NetworkBLAST: comparative analysis of protein networks , 2008 .
[58] Alan J. Laub,et al. Solution of the Sylvester matrix equation AXBT + CXDT = E , 1992, TOMS.
[59] R. Karp,et al. From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .
[60] 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.
[61] Ben Shneiderman,et al. Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis , 2003, 2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698).
[62] Santo Fortunato,et al. Community detection in graphs , 2009, ArXiv.
[63] Hans-Peter Kriegel,et al. Graph Kernels For Disease Outcome Prediction From Protein-Protein Interaction Networks , 2006, Pacific Symposium on Biocomputing.
[64] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[65] Eli Upfal,et al. Algorithms for Detecting Significantly Mutated Pathways in Cancer , 2010, RECOMB.
[66] Jean-Philippe Vert,et al. Graph kernels based on tree patterns for molecules , 2006, Machine Learning.
[67] Natasa Przulj,et al. Biological network comparison using graphlet degree distribution , 2007, Bioinform..
[68] Jacques van Helden,et al. Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.
[69] An-Yuan Guo,et al. A Novel microRNA and transcription factor mediated regulatory network in schizophrenia , 2010, BMC Systems Biology.
[70] O. Kuchaiev,et al. Topological network alignment uncovers biological function and phylogeny , 2008, Journal of The Royal Society Interface.
[71] R. Altman,et al. Whole-genome expression analysis: challenges beyond clustering. , 2001, Current opinion in structural biology.
[72] T. Ideker,et al. Modeling cellular machinery through biological network comparison , 2006, Nature Biotechnology.