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Virtual-organism toy-model as a tool to develop bioinformatics approaches of Systems Biology for medical-target discovery

Journal: ArXiv e-prints 2013, 1301.2528

Authors: Pujol A, Valls R, Radovanovic V, Guney E, Garcia-Garcia J, Domenech VC, Gonzalez LC, Mas JM, Oliva B

Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human cells. Since the Systems Biology still does not provide the most accurate answers to our questions due to the complexity of cells and the limited quality of available information to perform a good gene/protein map analysis, we have created simpler models to ensure easier analysis of the map that represents the human cell. Therefore, a virtual organism has been designed according to the main physiological rules for humans in order to replicate the human organism and its vital functions. This toy model was constructed by defining the topology of its genes/proteins and the biological functions associated to it. There are several examples of these toy models that emulate natural processes to perform analysis of the virtual life in order to design the best strategy to understand real life. The strategy applied in this study combines topological and functional analysis integrating the knowledge about the relative position of a node among the others in the map with the conclusions generated by mathematical models that reproduce functional data of the virtual organism. Our results demonstrate that the combination of both strategies allows better understanding of our virtual organism even with the lower input of information needed and therefore it can be a potential tool to better understand the real life.

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All Systems Go

Journal: European Biopharmaceutical Review 2013;June:44-47

Authors: Mas JM, Pujol A

In recent years, systems biology (SB) has arisen as a new discipline that aims to understand cell complexity by considering the available knowledge as a global system where the specific elements are less important than the global relationship between them. The maps generated by SB represent nature using two main strategies: those based on the topological information of the map (topological); and those that include the map but also any other functional information associated to a cell (functional). Using these approaches, it is possible to identify crucial points over the map that eventually become key proteins in cells, clarify the mechanisms of action and conduct drug repositioning. Unfortunately, the complexity of cells and the low quality of available data are two huge impediments to carrying out successful analyses. It is then necessary to create simpler models to determine the way of analysing the graph that represents the cell.

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Systems Biology Solutions to Microarray Nightmare

Journal: Innovations in Pharmaceutical Technology 2013;45:45-47

Authors: Sardón T, Segú C, Mas JM

Systems biology approaches may hold the key to overcoming the data analysis and interpretation difficulties from microarray technology. Here, a tool to understand a drug mechanism of action from a microarray experiment is outlined.

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Old Drug, New Tricks

Journal: European Biopharmaceutical Review 2012:21-22

Authors: Naval J, Mas JM

Systematic, bioinformatics-driven reprofiling offers an enticing way for companies to gain new value from old drugs. While approaches to this common goal vary, the initial results look promising.

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The New Science of Predictive Safety Testing

Journal: Innovations in Pharmaceutical Technology 2011 (March) 57-58

Authors: Naval J, Bigorra J

What price would a company pay to know that a compound in development had potential safety issues? New approaches to predictive safety aim to consider the whole complexity of human cellular biology by integrating all the available data, and ‘learning’ and reproducing the real behaviour of the system – the human body – using mathematical models.

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Systems Biology and Drug Regulation

Journal: PharmacoVigilance Review 2011;5(4):11-3

Authors: Farrés J, Bigorra J, Naval J

Systems biology approaches, through an interdisciplinary approach that combines experimental work with mathematical modelling, provide a new perspective for a better understanding of the drug responses, taking a mechanistic view of the involved processes. Although regulatory agencies reinforce the use of the new tools in the drug development process, it is still unclear how they will evaluate them and use them in the regulatory process.

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Biología de sistemas y nutrición. Efectos positivos de una dieta cetogénica rica en proteínas en pacientes con diabetes tipo II, de la evidencia clínica a la base molecular.

Journal: ALIMENTACION, NUTRICION Y SALUD 2011;18(2):7

Authors: Coma M, Mas JM, Molins A, Sajoux I, Fondevila J, Farrés J

Systems Biology approaches allow for an understanding of human physiology from a global perspective, cross cells, tissues or organs. The application of this type of approach into the nutrition and dietetics areas is only emerging. An example of this type of approach is the identification of the possible molecular mechanisms that explain the positive effects identified in the clinical practice of ketogenic diets enriched in proteins in diabetes type II patients. The analysis of the major relationships between molecules involved in the state of ketosis and diabetes type II highlights two complementary hypotheses: a) transportation and recycling of glucose transporter could be facilitated by certain proteins involved in metabolism lipid; and b) the inflammatory processes associated with insulin resistance can be seen relieved by the action of ketone bodies.

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Systems Biology footprint On the nutraceuticals and cosmetics arena

Journal: NutraFoods 2010;9(3):4

Authors: Naval J, Farrés J

Systems Biology, a new and validated integrative technology, finds many uses in the fields of cosmetics and nutraceuticals, accelerating the design of new products, and providing scientific support for health claims. Three practical situations are presented to illustrate how systems biology can be applied in the nutraceuticals and cosmetics area. 1 Positive relation between ketogenic diets and diabetes. 2 Cosmetics and skin aging. 3 Enhancing wellbeing effect.

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Systems biology upends drug reprofiling

Journal: Genetic Engineering and Biotechnology News 2010;30(18)

Authors: Coma M, Naval J.

There are smart thieves, and there are dumb thieves. Smart ones try to swiftly fit the right keys into the right locks, knowing which doors they wish to open. Dumb thieves try desperately to fit any kind of key into any kind of lock, no matter what door, and at the end they often get caught by the police.

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