Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data

(2012) Min Li et al.   BMC BIOINFORMATICS

Identifying Protein Complexes From Interactome Based on Essential Proteins and Local Fitness Method

(2012) Jianxin Wang et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Graph spectral analysis of protein interaction network evolution

(2012) T. Thorne et al.   Journal of the Royal Society Interface

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

(2012) Alexey I. Nesvizhskii   PROTEOMICS

A SURVEY OF COMPUTATIONAL METHODS FOR PROTEIN COMPLEX PREDICTION FROM PROTEIN INTERACTION NETWORKS

(2012) SRIGANESH SRIHARI et al.   Journal of Bioinformatics and Computational Biology

A comparison of the functional modules identified from time course and static PPI network data

(2011) Xiwei Tang et al.   BMC BIOINFORMATICS

Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data

(2011) Min Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ontology integration to identify protein complex in protein interaction networks

(2011) Bo Xu et al.   Proteome Science

Detecting protein complexes and functional modules from protein interaction networks: A graph entropy approach

(2011) Edward Casey Kenley et al.   PROTEOMICS

Identification of core-attachment complexes based on maximal frequent patterns in protein-protein interaction networks

(2011) Liang Yu et al.   PROTEOMICS

Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity

(2010) Jongkwang Kim et al.   BMC BIOINFORMATICS

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

(2010) Chen-Ching Lin et al.   BMC Systems Biology

Determining modular organization of protein interaction networks by maximizing modularity density

(2010) Shihua Zhang et al.   BMC Systems Biology

Toward the dynamic interactome: it's about time

(2010) T. M. Przytycka et al.   BRIEFINGS IN BIOINFORMATICS

A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks

(2010) Jianxin Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

(2010) P. J. Mucha et al.   SCIENCE

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

Enumeration of condition-dependent dense modules in protein interaction networks

(2009) Elisabeth Georgii et al.   BIOINFORMATICS

Complex discovery from weighted PPI networks

(2009) Guimei Liu et al.   BIOINFORMATICS

A core-attachment based method to detect protein complexes in PPI networks

(2009) Min Wu et al.   BMC BIOINFORMATICS

Protein complexes: the forest and the trees

(2009) Guillaume Adelmant et al.   Expert Review of Proteomics

Predicting Protein Complexes from PPI Data: A Core-Attachment Approach

(2009) Henry C.M. Leung et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast

(2009) Caroline C. Friedel et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Complex-based Reconstruction of theSaccharomyces cerevisiaeInteractome

(2009) Haidong Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Local Network Topology in Human Protein Interaction Data Predicts Functional Association

(2009) Hua Li et al.   PLoS One

Protein–protein interaction networks: how can a hub protein bind so many different partners?

(2009) Chung-Jung Tsai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

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

(2008) Min Li et al.   BMC BIOINFORMATICS

Evolution and dynamics of protein interactions and networks

(2008) Emmanuel D Levy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY

Interaction networks: From protein functions to drug discovery. A review

(2008) E. Chautard et al.   PATHOLOGIE BIOLOGIE

Quantitative function for community detection

(2008) Zhenping Li et al.   PHYSICAL REVIEW E

Are protein complexes made of cores, modules and attachments?

(2008) Chi Nam Ignatius Pang et al.   PROTEOMICS

Graph Clustering Via a Discrete Uncoupling Process

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

Response to Chatr-aryamontri et al.: Protein interactions: to believe or not to believe?

(2008) Joel P. Mackay et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein interactions: integration leads to belief

(2008) Andrew Chatr-aryamontri et al.   TRENDS IN BIOCHEMICAL SCIENCES

Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data

(2008) Shubhada R. Hegde et al.   PLoS Computational Biology