Traditional Chinese medicine (TCM) is the scientific therapeutics derived from the traditional Chinese physician's considerable clinical practice during the long history, with the characteristic of significant clinical therapeutic effects. The therapeutic philosophy of TCM is integrative medicine and pattern differentiation. The ideas of systems biology on the study of TCM were formed after the micro-and macro-outcome of systems biology being used into the practice of study on TCM. It is very important for the inheritance and development of TCM to disclose the basic mechanism of the clinical therapeutic effects of TCM and find new drugs, from the herbal preparation, pharmacology and pharmacokinetic to drug development using modern science technologies based on the theory of TCM.
Medicine, Chinese Traditional ; methods ; Systems Biology ; methods

Medicine, Chinese Traditional ; methods ; Systems Biology

The prevalence of coronary heart disease (CHD) is increasing, and has been a severe burden on society and family worldwide. New ideas need to be achieved for developing more efficacious and safe therapies to treat CHD. Chinese medicine (CM) uses multicomponent drugs to prevent disease and ameliorate symptoms based on patients' different syndromes. The benefit of CM in CHD has recently been proven by increasing clinical evidence. More importantly, linking CM syndrome differentiation and biomedical diagnosis might provide innovative thinking for treating CHD. According to epidemiological investigations, blood stasis syndrome (BSS) is the major type of syndrome in CHD. Investigating the biomedical mechanisms of BSS of CHD is a topic of CM research. Because the holistic perspective of systems biology is well matched with CM, the application of omics techniques and other integrative approaches appears inherently appropriate. A wide range of omics techniques, including transcriptomics and proteomics, have been used in studies of BSS of CHD to search for a common ground of understanding. These approaches could be useful for understanding BSS of CHD from clinical and biological viewpoints. Nevertheless, current studies mainly contain results from a single approach, and they have not achieved the holistic, systematic and integrative concept of system biology. Therefore, we discuss the progress and challenges in exploring the biomedical mechanisms of BSS of CHD by systems biology approaches. With further development of systems biology, a better platform to study BSS of CHD may be provided, and biomarkers for BSS of CHD and therapeutic targets may be found. The study of BSS of CHD by systems biology approaches will also be beneficial for developing personalized treatment for BSS of CHD patients.
Coronary Disease ; diagnosis ; metabolism ; Humans ; Syndrome ; Systems Biology ; methods

Secondary metabolites are produced during the growth and development of plants along with the adaptation of outer environment, as a rule they are the main active ingredients in medicinal plants and ensure the quality of crude drugs. Since biogenesis is quite complex, the production and accumulation of secondary metabolites are influenced by various biotic and abiotic factors either from gene or environments, the complexity may affect quality control of crude drugs and utilization of the active ingredients. The thought and approach adopted in systems biology is a powerful tool to explore biology fully, along with the development of modern molecular biology and information biology, omics integration like genomics, transcriptomics, proteomics, and metabolomics will bring new opportunities for the study of secondary metabolites of medicinal plant. It has great significance to apply this holistic and systematic method in researches on biosynthetic pathway, signal transduction, ecological environment and metabolic engineering of the formation of the secondary metabolites of medicinal plants, and in building secondary metabolite biosynthesis gene expression and regulation system model, in order to explain the origin of the active ingredients of medicinal plants, formation mechanism of the Chinese herbs, metabolic engineering effecting active ingredients of medicinal plants, and the rational exploitation and utilization of resources of medicinal plants systematically.
Models, Biological ; Models, Theoretical ; Plants, Medicinal ; metabolism ; Systems Biology ; methods

The development of new drug is not only the main driving force for the development of pharmaceutical industry, but also plays a very important role in the social development. However, with the increasing demands, new drug development is facing great difficulties in recent years. The hypothesis of highly selective single-target is meeting the challenges because of its limitations. Network pharmacology has been one of the new strategies for new drug discovery based on single-target drug research in recent years. This paper focused on the basis of network pharmacology and its research progress, discussed its development direction and application prospects, and analyzed its limitations and problems as well. The application of network pharmacology in new drug development is discussed by comparing its guidelines with those of traditional Chinese medicine theory and Effective Components Group hypothesis of Chinese medicines.
Algorithms ; Animals ; Computational Biology ; methods ; Drug Delivery Systems ; methods ; Drug Discovery ; methods ; Drug Interactions ; Humans ; Medicine, Chinese Traditional ; methods ; Software ; Systems Biology ; methods

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology--systemic structures, dynamics, control methods, and design principles.
Biological Evolution ; Gene Expression ; Genomics ; methods ; Models, Biological ; Systems Biology ; methods ; trends

Animals ; Cytological Techniques ; methods ; Cytophotometry ; instrumentation ; methods ; Humans ; Pharmacology ; methods ; trends ; Systems Biology ; methods ; Toxicology ; methods ; trends

Chronic kidney disease (CKD) is a major public health problem that affects about 10% of the general population. Current approaches to characterize the category and progression of CKD are normally based on renal histopathological results and clinical parameters. However, this information is not sufficient to predict CKD progression risk reliably or to guide preventive interventions. Nowadays, the appearance of systems biology has brought forward the concepts of "-omics" technologies, including genomics, transcriptomics, proteomics, and metabolomics. Systems biology, together with molecular analysis approaches such as microarray analysis, genome-wide association studies (GWAS), and serial analysis of gene expression (SAGE), has provided the framework for a comprehensive analysis of renal disease and serves as a starting point for generating novel molecular diagnostic tools for use in nephrology. In particular, analysis of urinary mRNA and protein levels is rapidly evolving as a non-invasive approach for CKD monitoring. All these systems biological molecular approaches are required for application of the concept of "personalized medicine" to progressive CKD, which will result in tailoring therapy for each patient, in contrast to the "one-size-fits-all" therapies currently in use.
Computational Biology ; Gene Expression Profiling ; Genome-Wide Association Study ; Humans ; Renal Insufficiency, Chronic ; genetics ; metabolism ; Systems Biology ; methods

Biofuels are renewable and environmentally friendly, but high production cost makes them economically not competitive, and the development of robust strains is thus one of the prerequisites. In this article, strain improvement studies based on the information from systems biology studies are reviewed, with a focus on their applications on stress tolerance improvement. Furthermore, the contribution of systems biology, synthetic biology and metabolic engineering in strain development for biofuel production is discussed, with an expectation for developing more robust strains for biofuel production.
Biofuels ; Genetic Engineering ; methods ; Industrial Microbiology ; methods ; trends ; Lignin ; metabolism ; Saccharomyces cerevisiae ; genetics ; metabolism ; physiology ; Synthetic Biology ; methods ; Systems Biology ; methods

Along with progress of modern science and technology, human is utilizing natural resources and their inherent law more effectively and more efficiently according to their own purposes. Chinese medicine pair (CMP) is relatively fixed combination of two TCMs which was proven to be effective in clinical application. CMP has its inner specification, and it is an intermediate point between single herb and many TCM formulae. With the aid of modern science and technology, and by means of choosing appropriate strategies and approaches, the compatibility rules of CMP might be revealed, which will be significant to develop the compatibility theory of TCM formulae and create modern TCM new drugs.
Animals ; Clinical Trials as Topic ; Drug Interactions ; Humans ; Medicine, Chinese Traditional ; methods ; Research Design ; Systems Biology