The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be
integrated with other data. One approach to integration is through the annotation of multiple …
integrated with other data. One approach to integration is through the annotation of multiple …
Network analyses in systems pharmacology
SI Berger, R Iyengar - Bioinformatics, 2009 - academic.oup.com
Abstract Systems pharmacology is an emerging area of pharmacology which utilizes
network analysis of drug action as one of its approaches. By considering drug actions and …
network analysis of drug action as one of its approaches. By considering drug actions and …
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …
Among these associations, protein–protein interactions are particularly important due to their …
Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy
This study examined the microbial diversity and community assembly of oral microbiota in
periodontal health and disease and after nonsurgical periodontal treatment. The V4 region …
periodontal health and disease and after nonsurgical periodontal treatment. The V4 region …
Integration of biological networks and gene expression data using Cytoscape
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …
Chapter 5: Network biology approach to complex diseases
DY Cho, YA Kim, TM Przytycka - PLoS computational biology, 2012 - journals.plos.org
Complex diseases are caused by a combination of genetic and environmental factors.
Uncovering the molecular pathways through which genetic factors affect a phenotype is …
Uncovering the molecular pathways through which genetic factors affect a phenotype is …
Exploring local community structures in large networks
In this paper, three new algorithms, a greedy algorithm, a KL-like algorithm, and an add-all
algorithm, are proposed to find local optimal community structures in large networks starting …
algorithm, are proposed to find local optimal community structures in large networks starting …
A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
As advances in the technologies of predicting protein interactions, huge data sets portrayed
as networks have been available. Identification of functional modules from such networks is …
as networks have been available. Identification of functional modules from such networks is …
CytoCluster: a cytoscape plugin for cluster analysis and visualization of biological networks
Nowadays, cluster analysis of biological networks has become one of the most important
approaches to identifying functional modules as well as predicting protein complexes and …
approaches to identifying functional modules as well as predicting protein complexes and …
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data
Background Identification of protein complexes and functional modules from protein-protein
interaction (PPI) networks is crucial to understanding the principles of cellular organization …
interaction (PPI) networks is crucial to understanding the principles of cellular organization …