Springer protocols feed by Bioinformatics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Modeling and Simulation Tools: From Systems Biology to Systems Medicine
Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of “Software as a Medical Device” and what this may imply for the migration of research-oriented, simulation software into the domain of human health. (Source: Sprin...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study
We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non-exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine
Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases. Complex diseases arise from the interactions among disease-influencing factors across multiple levels of biological organization from the environment to molecules. To tackle the enormous challenges posed by complex diseases, we need a modeling and simulation framework capable of capturing and integrating information originating...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Network-Assisted Disease Classification and Biomarker Discovery
Developing improved approaches for diagnosis, treatment, and prevention of diseases is a major goal of biomedical research. Therefore, the discovery of biomarker signatures from high-throughput “omics” data is an active research topic in the field of bioinformatics and systems medicine. A major issue is the low reproducibility and the limited biological interpretability of candidate biomarker signatures identified from high-throughput data. This impedes the use of discovered biomarker signatures into clinical applications. Currently, much focus is placed on developing strategies to improve reproducibility and i...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine
Regenerative medicine, ranging from stem cell therapy to organ regeneration, is promising to revolutionize treatments of diseases and aging. These approaches require a perfect understanding of cell reprogramming and differentiation. Predictive modeling of cellular systems has the potential to provide insights about the dynamics of cellular processes, and guide their control. Moreover in many cases, it provides alternative to experimental tests, difficult to perform for practical or ethical reasons. The variety and accuracy of biological processes represented in mathematical models grew in-line with the discovery of underly...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
RNA Systems Biology for Cancer: From Diagnosis to Therapy
It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to th...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD
In conclusion, in our hands the scope and efforts of systems medicine need to concurrently consider these aspects of clinical implementation, which inherently drives the selection of the most relevant and urgent issues and methods that need further development in a systems analysis of disease. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine
Modern high-throughput techniques offer immense opportunities to investigate whole-systems behavior, such as those underlying human diseases. However, the complexity of the data presents challenges in interpretation, and new avenues are needed to address the complexity of both diseases and data. Constraint-based modeling is one formalism applied in systems biology. It relies on a genome-scale reconstruction that captures extensive biochemical knowledge regarding an organism. The human genome-scale metabolic reconstruction is increasingly used to understand normal cellular and disease states because metabolism is an importa...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive
The understanding of the immune response is right now at the center of biomedical research. There are growing expectations that immune-based interventions will in the midterm provide new, personalized, and targeted therapeutic options for many severe and highly prevalent diseases, from aggressive cancers to infectious and autoimmune diseases. To this end, immunology should surpass its current descriptive and phenomenological nature, and become quantitative, and thereby predictive. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Systems Medicine for Lung Diseases: Phenotypes and Precision Medicine in Cancer, Infection, and Allergy
Lung diseases cause an enormous socioeconomic burden. Four of them are among the ten most important causes of deaths worldwide: Pneumonia has the highest death toll of all infectious diseases, lung cancer kills the most people of all malignant proliferative disorders, chronic obstructive pulmonary disease (COPD) ranks third in mortality among the chronic noncommunicable diseases, and tuberculosis is still one of the most important chronic infectious diseases. Despite all efforts, for example, by the World Health Organization and clinical and experimental researchers, these diseases are still highly prevalent and harmful. T...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Systems Medicine and Infection
By using a systems-based approach, mathematical and computational techniques can be used to develop models that describe the important mechanisms involved in infectious diseases. An iterative approach to model development allows new discoveries to continually improve the model and ultimately increase the accuracy of predictions. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Neurological Diseases from a Systems Medicine Point of View
The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurologica...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Systems Medicine in Oncology: Signaling Network Modeling and New-Generation Decision-Support Systems
Two different perspectives are the main focus of this book chapter: (1) A perspective that looks to the future, with the goal of devising rational associations of targeted inhibitors against distinct altered signaling-network pathways. This goal implies a sufficiently in-depth molecular diagnosis of the personal cancer of a given patient. A sufficiently robust and extended dynamic modeling will suggest rational combinations of the abovementioned oncoprotein inhibitors. The work toward new selective drugs, in the field of medicinal chemistry, is very intensive. Rational associations of selective drug inhibitors will become ...
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Systems Medicine in Pharmaceutical Research and Development
The development of new drug therapies requires substantial and ever increasing investments from the pharmaceutical company. Ten years ago, the average time from early target identification and optimization until initial market authorization of a new drug compound took more than 10 years and involved costs in the order of one billion US dollars. Recent studies indicate even a significant growth of costs in the meanwhile, mainly driven by the increasing complexity of diseases addressed by pharmaceutical research. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
Training in Systems Approaches for the Next Generation of Life Scientists and Medical Doctors
We describe the current challenges and scattered best practices of introducing the wider systems medicine topics into the medical education as well as possibilities for systems medicine training at the doctoral and lifelong levels. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - December 21, 2015 Category: Bioinformatics Source Type: news
