Systems biology visualization tools for drug target discovery

  title={Systems biology visualization tools for drug target discovery},
  author={Tianxiao Huan and Xiaogang Wu and Jake Yue Chen},
  journal={Expert Opinion on Drug Discovery},
  pages={425 - 439}
Importance of the field: Post-genome drug development has been driven by the need to study biological perturbations at the molecular system level. Systems biology visualization tools can help researchers extract hidden patterns from complex and large Omics data sets, model disease molecular mechanisms, and identify drug targets and drugs with good pharmacological and toxicological profiles. Areas covered in this review: This review covers basic concepts in developing and applying information… 
Systems Pharmacology: A Unified Framework for Prediction of Drug-Target Interactions.
By presenting the unified framework and the integrated scheme, underlying computational methods for problems in systems pharmacology can be understood and complex relationships among diseases, genes and drugs can be identified effectively.
Simulation and Visual Analysis of Neuromusculoskeletal Models and Data
This work presents a novel medical decision support system for diseases related to the upper body neuromusculature and uses visual analytics metaphors and in particular both embodied and symbolic visualizations to demonstrate the analytics potential of the proposed system.
The shortest path is not the one you know: application of biological network resources in precision oncology research.
This review describes the available biological pathway resources, their characteristics in terms of construction mode, focus, aims and paradigms of biological knowledge representation, and presents a new resource that is focused on cancer-related signalling, the Atlas of Cancer Signalling Networks.
Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine
The history and research trends of pharmacogenomics, systems biology, and personalized medicine are examined, and bioethical concerns that arise from dealing with the increasing accumulation of biological samples in many biobanking projects today are presented.


Systems biology in drug discovery
Automation of complex primary human cell–based assay systems designed to capture emergent properties can now integrate a broad range of disease-relevant human biology into the drug discovery process, informing target and compound validation, lead optimization, and clinical indication selection.
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology and can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches.
Tools for visually exploring biological networks
This work provides a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools.
BiologicalNetworks: visualization and analysis tool for systems biology
A server, BiologicalNetworks, is described, which provides visualization, analysis services and an information management framework over PathSys, which allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein–protein, protein–DNA and genetic interactions.
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining
ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies and is suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations.
Protein interactions and disease: computational approaches to uncover the etiology of diseases
  • M. Kann
  • Biology
    Briefings Bioinform.
  • 2007
This review explores recent approaches to the understanding of the mechanisms of disease at the molecular level through their underlying protein interactions through genetics, protein structure and protein interaction network analyses.
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
The Annotation, Mapping, Expression and Network (AMEN) software is developed as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data.
An Evaluation of Microarray Visualization Tools for Biological Insight
This paper empirically evaluate five popular microarray visualization tools and identifies several distinct characteristics of insight that enable us to recognize and quantify it, and can guide biologists in selecting the best tool for their data, and computer scientists in developing and evaluating visualizations.
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
A free stand-alone computer program designed for viewing and analyzing gene expression data in the context of biological pathways, GenMAPP (Gene Microarray Pathway Profiler), which complements the current pathway databases by providing a means of freely exchanging pathway-related data among investigators.
JNets: Exploring networks by integrating annotation
JNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page, and highlights the intricate influence that HIV-1 has on the host immune response.