[PDF] Top 20 Modularity detection in protein protein interaction networks
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Modularity detection in protein protein interaction networks
... One such divisive technique of interest is the Newman and Girvan (NG) algorithm [1], which uses the notion of edge-betweenness, a metric that has received consider- able recent research interest in the domain of modular- ... See full document
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Modular organization in the reductive evolution of protein protein interaction networks
... of modularity of the protein inter- action ...reduced modularity in the Buch- nera genome is caused by the partial deletion of nodes in regions that are connected to dense clusters of essential func- ... See full document
8
Complex tree: the basic framework of protein protein interaction networks
... In the past few years, notable discoveries of exploring complex networks have redefined our understanding of complex systems. Meanwhile, certain models have been constructed to mimic real networks [20-24]. ... See full document
7
Construction of Protein Protein Interaction Network Using Community Molecular Detection
... PPI detection are tandem affinity purification, affinity chromatography, protein arrays, protein fragment complementation, phage display, X-ray crystallography, and NMR ...PPI detection are ... See full document
12
Local pre-processing for node classification in networks : application in protein-protein interaction
... social networks [1], protein structures and interactions [3], genetic control [20], market economies [21] and human and machine communi- cation ...social networks [1] or periods of excessive workload ... See full document
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Detecting Protein Complexes by an Improved Affinity Propagation Algorithm in Protein-Protein Interaction Networks
... These above methods mainly focus on extracting the dense sub-graphs and discarding relatively sparse ones. As a result, many complexes are missed. Partition based clustering algorithms can overcome this difficulty. For ... See full document
8
FAC-PIN: An efficient and fast agglomerative clustering algorithm for protein interaction networks to predict protein complexes and functional modules
... used protein interaction networks of sixteen different ...each protein interaction network for each α, a mathematical function is used to evaluate the clusters of a protein ... See full document
85
Construction and Analysis of Tissue-Specific Protein-Protein Interaction Networks in Humans
... The formal representation of PINs as undirected graphs makes it possible to utilize a variety of well-established graph measures. We have computed 12 individual graph measures that reflect the following graph properties: ... See full document
13
Simplified Swarm Optimization Based Function Modules Detection in Protein-to-Protein Interaction Networks
... Biomolecular Interaction Network Database (BIND) [9], Database of Interaction Proteins (DIP) [10], IntAct [11], Human Protein Reference Database (HPRD) [12], and Molecular Interaction Database ... See full document
13
Identification of protein complexes from multi-relationship protein interaction networks
... identification protein com- plexes are still a ...of protein complex detection ...discover protein complexes with core- attachment structures from tandem affinity purification (TAP) data ... See full document
10
Protein complex detection with semi-supervised learning in protein interaction networks
... detected protein com- plexes in protein-protein interaction networks from a different ...PPI networks, we proposed a semi-supervised prediction model with neural ...represent ... See full document
9
A novel functional module detection algorithm for protein-protein interaction networks
... between protein function and PPI is characterized by weak connectivity and unexpected topological phenomena, such as low intraconnectivity and longish shapes of actual topological shapes of MIPS functional ... See full document
11
Ontology integration to identify protein complex in protein interaction networks
... of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection ...of protein-protein ... See full document
10
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks
... 12 protein complexes were known to be associated with prostate cancer (See in Additional file 1: Table ...associated protein complexes were set as source nodes and all others as candidates in ...selected ... See full document
12
Time Evolving Undirected Graphical Model for Protein-Protein Interaction Networks
... The Human protein-protein interaction data file “Hsapi20170205.txt” from DIP database was used [32, 33] for analyzing. All DIP database records available through this Web Site are freely available ... See full document
11
Assortativity of aging key players in the dynamical networks
... Aging process continues from younger to older people as many factors contribute to accelerate or decelerate the process. However, this biological process is poorly understood and therefore, aging- related genes gain more ... See full document
15
Molecular docking as a popular tool in drug design, an in silico travel
... of protein interface water prediction and show that further work is needed to attain a performance that is of practical use for drug design ...the protein–protein interface hotspot, were ... See full document
11
Protein-protein interaction networks: probing disease mechanisms using model systems
... The vast majority of MS-based studies of PPIs in human cells have been performed under tissue-culture con- ditions using a few representative cell lines, the vast majority of which are cancer-derived or transformed. ... See full document
12
Evaluating Joint Modeling of Yeast Biology Literature and Protein Protein Interaction Networks
... articles and yeast protein-protein interaction networks. The topic coherence of the emer- gent topics and the ability of the model to re- trieve relevant scientific articles and proteins ... See full document
8
Friedel, Caroline Christina (2009): Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. Dissertation, LMU München: Fakultät für Mathematik, Informatik und Statistik
... The sampling procedure described by Han et al. (2005) corresponds to an experimen- tal setting in which only a small set of proteins is chosen as baits and then subsequently screened against a much larger set of preys. ... See full document
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