Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin
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[1] Han Zhao,et al. Global network alignment in the context of aging , 2015, TCBB.
[2] Jugal K. Kalita,et al. A comparison of algorithms for the pairwise alignment of biological networks , 2014, Bioinform..
[3] Natasa Przulj,et al. Integrative network alignment reveals large regions of global network similarity in yeast and human , 2011, Bioinform..
[4] Roded Sharan,et al. Fast and Accurate Alignment of Multiple Protein Networks , 2009, J. Comput. Biol..
[5] Andrea Lancichinetti,et al. Community detection algorithms: a comparative analysis: invited presentation, extended abstract , 2009, VALUETOOLS.
[6] Robert Patro,et al. Global network alignment using multiscale spectral signatures , 2012, Bioinform..
[7] Jiong Guo,et al. GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment , 2013, GCB.
[8] Cesim Erten,et al. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks , 2014, Bioinform..
[9] Jie Tang,et al. Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE , 2014, WABI.
[10] Knut Reinert,et al. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks , 2014, Bioinform..
[11] Xin Li,et al. Phylogenetic analysis of modularity in protein interaction networks , 2009, BMC Bioinformatics.
[12] Aaron Striegel,et al. IGLOO: Integrating global and local biological network alignment , 2016, 1604.06111.
[13] Vipin Vijayan,et al. Multiple Network Alignment via MultiMAGNA++ , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[14] Wojciech Szpankowski,et al. Pairwise Alignment of Protein Interaction Networks , 2006, J. Comput. Biol..
[15] Tijana Milenkovic,et al. MAGNA: Maximizing Accuracy in Global Network Alignment , 2013, Bioinform..
[16] Ozlem Keskin,et al. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces , 2008, Briefings Bioinform..
[17] Jiong Guo,et al. Multiple graph edit distance: simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm , 2014, GECCO.
[18] Jaap Heringa,et al. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment , 2015, Algorithms.
[19] Mohammadmahdi R. Yousefi,et al. Optimal cancer prognosis under network uncertainty , 2015, EURASIP journal on bioinformatics & systems biology.
[20] Mario Cannataro,et al. IMPRECO: Distributed prediction of protein complexes , 2010, Future Gener. Comput. Syst..
[21] R. Guimerà,et al. Use of a global metabolic network to curate organismal metabolic networks , 2013, Scientific Reports.
[22] Mario Cannataro,et al. Protein-to-protein interactions: Technologies, databases, and algorithms , 2010, CSUR.
[23] Arnaud Céol,et al. NetAligner—a network alignment server to compare complexes, pathways and whole interactomes , 2012, Nucleic Acids Res..
[24] Natasa Przulj,et al. Fuse: multiple network alignment via data fusion , 2014, Bioinform..
[25] F. Radicchi,et al. Benchmark graphs for testing community detection algorithms. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[26] Jugal K. Kalita,et al. A multiobjective memetic algorithm for PPI network alignment , 2015, Bioinform..
[27] Pietro Hiram Guzzi,et al. AlignMCL: Comparative analysis of protein interaction networks through Markov clustering , 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.
[28] Rahul Singh,et al. The SMAL web server: global multiple network alignment from pairwise alignments , 2016, Bioinform..
[29] Jan Martens,et al. NABEECO: biological network alignment with bee colony optimization algorithm , 2013, GECCO.
[30] Tijana Milenkovic,et al. GREAT: GRaphlet Edge-based network AlignmenT , 2014, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[31] Elena Marchiori,et al. A methodology for detecting the orthology signal in a PPI network at a functional complex level , 2012, BMC Bioinformatics.
[32] 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.
[33] Gunnar W. Klau,et al. A new graph-based method for pairwise global network alignment , 2009, BMC Bioinformatics.
[34] Benno Schwikowski,et al. Graph-based methods for analysing networks in cell biology , 2006, Briefings Bioinform..
[35] Elaine Shi,et al. Link prediction by de-anonymization: How We Won the Kaggle Social Network Challenge , 2011, The 2011 International Joint Conference on Neural Networks.
[36] Pietro Hiram Guzzi,et al. Improving the Robustness of Local Network Alignment: Design and Extensive Assessmentof a Markov Clustering-Based Approach , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[37] Tijana Milenkovic,et al. Dynamic networks reveal key players in aging , 2014, BCB.
[38] Simona E. Rombo,et al. Searching for repetitions in biological networks: methods, resources and tools , 2015, Briefings Bioinform..
[39] Lei Meng,et al. The post-genomic era of biological network alignment , 2015, EURASIP J. Bioinform. Syst. Biol..
[40] Aaron Striegel,et al. Local versus global biological network alignment , 2015, Bioinform..
[41] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[42] Roded Sharan,et al. NetworkBLAST: comparative analysis of protein networks , 2008 .
[43] Bonnie Berger,et al. Local Optimization for Global Alignment of Protein Interaction Networks , 2010, Pacific Symposium on Biocomputing.
[44] R. Karp,et al. From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .
[45] Chuan Yi Tang,et al. Reconstruction of phyletic trees by global alignment of multiple metabolic networks , 2013, BMC Bioinformatics.
[46] Philip S. Yu,et al. COSNET: Connecting Heterogeneous Social Networks with Local and Global Consistency , 2015, KDD.
[47] Mary Ellen Bock,et al. I STITUTO DI A NALISI DEI S ISTEMI ED I NFORMATICA “ Antonio Ruberti , 2012 .
[48] Nil Mamano,et al. SANA: Simulated Annealing Network Alignment Applied to Biological Networks , 2016, 1607.02642.
[49] Stephen A. Cook,et al. The complexity of theorem-proving procedures , 1971, STOC.
[50] Santo Fortunato,et al. Community detection in graphs , 2009, ArXiv.
[51] 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.
[52] Behnam Neyshabur,et al. NETAL: a new graph-based method for global alignment of protein-protein interaction networks , 2013, Bioinform..
[53] Vesna Memi. Complementarity of network and sequence information in homologous proteins , 2010 .
[54] Yihan Sun,et al. Fair evaluation of global network aligners , 2014, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[55] Jianzhu Ma,et al. ModuleAlign: module-based global alignment of protein-protein interaction networks , 2016, Bioinform..
[56] Philip S. Yu,et al. Multiple Anonymized Social Networks Alignment , 2015, 2015 IEEE International Conference on Data Mining.
[57] Haiyuan Yu,et al. Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.
[58] Tolga Can,et al. SUMONA: A supervised method for optimizing network alignment , 2016, Comput. Biol. Chem..
[59] Jugal K. Kalita,et al. Global Alignment of Protein-Protein Interaction Networks: A Survey , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[60] Pietro Hiram Guzzi,et al. MODULA: A network module based local protein interaction network alignment method , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[61] C. Croce,et al. MicroRNA-cancer connection: the beginning of a new tale. , 2006, Cancer research.
[62] M. Cannataro,et al. AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology , 2012, PloS one.
[63] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[64] Byung-Jun Yoon,et al. SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks , 2013, PloS one.
[65] Tijana Milenkovic,et al. MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation , 2015, Bioinform..
[66] George C. Verghese,et al. Graph similarity scoring and matching , 2008, Appl. Math. Lett..
[67] Tijana Milenkoviæ,et al. Uncovering Biological Network Function via Graphlet Degree Signatures , 2008, Cancer informatics.
[68] Mario Cannataro,et al. Semantic similarity analysis of protein data: assessment with biological features and issues , 2012, Briefings Bioinform..
[69] Bonnie Berger,et al. IsoRankN: spectral methods for global alignment of multiple protein networks , 2009, Bioinform..
[70] Giovanni Micale,et al. GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks , 2014, PloS one.
[71] Natasa Przulj,et al. L-GRAAL: Lagrangian graphlet-based network aligner , 2015, Bioinform..
[72] U. Alon. Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.
[73] O. Kuchaiev,et al. Topological network alignment uncovers biological function and phylogeny , 2008, Journal of The Royal Society Interface.