1. Introduction to Biomedical Engineering Tutor: Susana Vinga, INESC-ID/FCM-UNL Master in Biomedical Engineering, IST/FML 2011/2012 Ana de Aguiar nº 72727; Carolina Veiga nº 72895; João Lopes nº 72845; Vanessa Lopes nº73107

2.  Pneumococcal diseases ◦ Streptococcus pneumoniae  Pathogenic bacterium ◦ Diseases: can be both harmless (upper respiratory tract) and fatal (lungs, blood stream, meninges). ◦ Prevention  vaccines ◦ Epidemiology  Responsible for more than a million of death (826000 in children and a top 10 cause of death in USA) Modeling Pneumococcal disease Using a Systems Biology Approach 11/122 In: http://www.sciencephoto.com/media/12983/enlarge

3. Modeling Pneumococcal disease Using a Systems Biology Approach 11/123 Pneumococcal deaths in children aged 1–59 months per 100 000 children younger than 5 years (HIV- negative pneumococcal deaths only). In: O’Brien, Wolfson et. al., Lancet 2009

4.  Mathematical and computational modelling ◦ How sugar metabolism influences bacteria colonization and invasion ◦ How the gene regulatory network interacts with metabolic network Modeling Pneumococcal disease Using a Systems Biology Approach 11/124 Systems Biology

5.  Studies interactions between all elements of biological systems, which are responsible for its functions and behaviour.  E.g.: Proteomics identify and quantify the cellular levels of each protein that is encoded by the genome. Modeling Pneumococcal disease Using a Systems Biology Approach 11/125 In: Joyce and Palsson, Nat Rev Mol Cell Biol 2006 1 2 3

6. In: http://www.popsci.com/scitech/article/2 009-02/so-do-you-really-want-know http://www.popsci.com/scitech/article/2 009-02/so-do-you-really-want-know  1. Genomics ◦ Gene sequencing methods, DNA databases;  2. Transcriptomics ◦ Microarray technology and clustering;  3. Metabolomics ◦ Growth curves, mutant vs. wild type  MATLAB simulation Modeling Pneumococcal disease Using a Systems Biology Approach 11/126 In: Carvalho, Kloosterman et. al., 2011

7. Project Goal Analysis of mathematical and computational methods suitable to create predictable and interpretable biological networks for medical application. Modeling Pneumococcal disease Using a Systems Biology Approach 11/127

8. Planning Search clinical and epidemiological data of pneumococcal diseases Study of methods and concepts of Systems Biology Collection of dynamic models of growth curves and data expression review Simulation and analysis of the referred models using MATLAB Modeling Pneumococcal disease Using a Systems Biology Approach 11/128 Web search Article reading Presentations by inesc-id researchers Article reading Presentations by inesc-id researchers MATLAB tutorial