GA-PPI-Net Approach vs Analytical Approaches for Community Detection in PPI Networks

[1]  Andrea Lancichinetti,et al.  Detecting the overlapping and hierarchical community structure in complex networks , 2008, 0802.1218.

[2]  Judith A. Blake,et al.  Gene Ontology annotations: what they mean and where they come from , 2008, BMC Bioinformatics.

[3]  S. Fortunato,et al.  Resolution limit in community detection , 2006, Proceedings of the National Academy of Sciences.

[4]  Haiyuan Yu,et al.  Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.

[5]  Xin Liu,et al.  Effective Algorithm for Detecting Community Structure in Complex Networks Based on GA and Clustering , 2007, International Conference on Computational Science.

[6]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[7]  Rod K. Nibbe,et al.  Protein–protein interaction networks and subnetworks in the biology of disease , 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

[8]  Keith C. C. Chan,et al.  Evolutionary Graph Clustering for Protein Complex Identification , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[9]  Philip S. Yu,et al.  COMPARISON AND SELECTION OF OBJECTIVE FUNCTIONS IN MULTIOBJECTIVE COMMUNITY DETECTION , 2014, Comput. Intell..

[10]  Igor Jurisica,et al.  Protein complex prediction via cost-based clustering , 2004, Bioinform..

[11]  Clara Pizzuti,et al.  GA-Net: A Genetic Algorithm for Community Detection in Social Networks , 2008, PPSN.

[12]  David Liu,et al.  DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis , 2007, BMC Bioinformatics.

[13]  Qing Liao,et al.  A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks , 2019, Briefings Bioinform..

[14]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  Luay Nakhleh,et al.  GS2: an efficiently computable measure of GO-based similarity of gene sets , 2009, Bioinform..

[16]  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.

[17]  Luonan Chen,et al.  Quantitative function for community detection. , 2008 .

[18]  Clara Pizzuti,et al.  A Multiobjective Genetic Algorithm to Find Communities in Complex Networks , 2012, IEEE Transactions on Evolutionary Computation.

[19]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[20]  S. Dongen Graph clustering by flow simulation , 2000 .

[21]  Claudio Castellano,et al.  Defining and identifying communities in networks. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Jing Dong,et al.  Ontology Classification for Semantic-Web-Based Software Engineering , 2009, IEEE Transactions on Services Computing.

[23]  Christian von Mering,et al.  STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..

[24]  Jacques van Helden,et al.  Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.

[25]  B. Snel,et al.  STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. , 2000, Nucleic acids research.

[26]  Haluk Bingol,et al.  Community Detection in Complex Networks Using Genetic Algorithms , 2006, 0711.0491.

[27]  Maoguo Gong,et al.  A survey on network community detection based on evolutionary computation , 2016, Int. J. Bio Inspired Comput..

[28]  Amel Borgi,et al.  Genetic Algorithm to Detect Different Sizes' Communities from Protein-Protein Interaction Networks , 2019, ICSOFT.

[29]  Halife Kodaz,et al.  Community detection from biological and social networks: A comparative analysis of metaheuristic algorithms , 2017, Appl. Soft Comput..

[30]  Rohan Agrawal,et al.  Bi-Objective Community Detection (BOCD) in Networks Using Genetic Algorithm , 2011, IC3.

[31]  Phillip W. Lord,et al.  Semantic Similarity in Biomedical Ontologies , 2009, PLoS Comput. Biol..

[32]  Clara Pizzuti,et al.  Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods , 2014, Bioinform..

[33]  Clara Pizzuti,et al.  Evolutionary Computation for Community Detection in Networks: A Review , 2018, IEEE Transactions on Evolutionary Computation.