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Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework.Expand
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Cytoscape 2.8: new features for data integration and network visualization
TLDR
We introduce two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Expand
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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 results of mRNAExpand
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Genome-wide methylation profiles reveal quantitative views of human aging rates.
The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics, and extension of life. AlthoughExpand
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A travel guide to Cytoscape plugins
TLDR
We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.8. Expand
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Network-based classification of breast cancer metastasis
Mapping the pathways that give rise to metastasis is one of the key challenges of breast cancer research. Recently, several large‐scale studies have shed light on this problem through analysis ofExpand
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A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 millionExpand
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Discovering regulatory and signalling circuits in molecular interaction networks
TLDR
We introduce an approach for screening a molecular interaction network to identify active subnetworks, i.e., connected regions of the network that show significant changes in expression over particular subsets of conditions. Expand
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Network-based stratification of tumor mutations
Many forms of cancer have multiple subtypes with different causes and clinical outcomes. Somatic tumor genome sequences provide a rich new source of data for uncovering these subtypes but have provenExpand
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Inferring Pathway Activity toward Precise Disease Classification
TLDR
We propose a novel gene-expression-based diagnostic that incorporates pathway information in a condition-specific manner (Pathway Activity inference using Condition-responsive genes, PAC). Expand
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