[Applications of elementary mode analysis in biological network and pathway analysis]
Quanyu Zhao1, Shuiyan Yu, Jiping Shi
1Biorefinery Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China. zhaoqy@sari.ac.cn
Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology
|September 26, 2013
Summary
Elementary mode analysis (EMA) is a key tool for understanding metabolic and signal transduction networks across systems from cells to ecosystems. This review covers EMA algorithms, applications, and future research directions for metabolic pathway analysis.
Area of Science:
- Systems Biology
- Metabolic Engineering
- Bioinformatics
Context:
- Elementary mode analysis (EMA) is a widely applied computational tool for metabolic pathway analysis.
- EMA is utilized for both metabolic and signal transduction networks, applicable from cellular to ecological systems.
- It can describe biological behaviors using steady-state and dynamic models, evaluating microorganism metabolism and human health.
Purpose:
- To review the algorithms and software for calculating elementary modes (EM).
- To provide a comprehensive overview of EMA applications in various biological contexts.
- To identify key challenges and future research directions for EMA.
Summary:
- This study analyzes algorithms and software for elementary mode (EM) calculation.
- It reviews diverse EMA applications, including metabolic pathway analysis, network robustness, flux decomposition, bioprocess simulation, and signal transduction.
- EMA provides insights into microorganism metabolism and human health.
Impact:
- Provides a foundational understanding of elementary mode analysis for researchers.
- Highlights the versatility of EMA in systems biology and metabolic engineering.
- Identifies critical areas for future research, such as improving computational efficiency and exploring regulatory relationships.
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