Algorithms and tools for protein–protein interaction networks clustering, with a special focus on population-based stochastic methods

Graphlet-based edge clustering reveals pathogen-interacting proteins

(2012) R. W. Solava et al.   BIOINFORMATICS

A methodology for detecting the orthology signal in a PPI network at a functional complex level

(2012) Pavol Jancura et al.   BMC BIOINFORMATICS

Comparative analysis of protein networks

(2012) Nir Atias et al.   COMMUNICATIONS OF THE ACM

Multifunctional proteins revealed by overlapping clustering in protein interaction network

(2011) Emmanuelle Becker et al.   BIOINFORMATICS

GraphCrunch 2: Software tool for network modeling, alignment and clustering

(2011) Oleksii Kuchaiev et al.   BMC BIOINFORMATICS

Asymmetric Comparison and Querying of Biological Networks

(2011) N Ferraro et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Coclustering Approach for Mining Large Protein-Protein Interaction Networks

(2011) C. Pizzuti et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Computational approaches for detecting protein complexes from protein interaction networks: a survey

(2010) Xiaoli Li et al.   BMC GENOMICS

Line graphs of weighted networks for overlapping communities

(2010) T. S. Evans et al.   EUROPEAN PHYSICAL JOURNAL B

Link communities reveal multiscale complexity in networks

(2010) Yong-Yeol Ahn et al.   NATURE

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics

(2010) István A. Kovács et al.   PLoS One

Enumeration of condition-dependent dense modules in protein interaction networks

(2009) Elisabeth Georgii et al.   BIOINFORMATICS

RRW: repeated random walks on genome-scale protein networks for local cluster discovery

(2009) Kathy Macropol et al.   BMC BIOINFORMATICS

Line graphs, link partitions, and overlapping communities

(2009) T. S. Evans et al.   PHYSICAL REVIEW E

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

(2008) Min Li et al.   BMC BIOINFORMATICS

Identifying network communities with a high resolution

(2008) Jianhua Ruan et al.   PHYSICAL REVIEW E

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS