Computational Systems Biology Laboratory
|
Laboratory Name |
Computational System Biology Laboratory |
| Laboratory Responsible | Assoc. Prof. Dr. Tunahan ÇAKIR Assist. Prof. Dr. Saliha DURMUŞ Assist. Prof. Dr. Pınar PİR |
| Department | Department of Bioengineering |
| Telephone | (+90) 262 605 33 20 |
| Adress |
Gebze Institute of Technology, Department of Bioengineering, 41400, |
| Web Page | |
| Laboratory Staff |
Res. Assist. Gülben Avşar (PhD Student) |
| General Information | The research conducted in Computational Systems Biology Laboratory aims to apply a systems biology approach to understand the principles of cellular functioning and the disease mechanisms by investigating cellular networks via bioinformatics-based computational methods. Within this scope, research in our laboratory focuses on:
and uses genome-wide data (genome, transcriptome) and genome-scale molecular interaction networks (metabolic networks, protein interaction networks) integratively for the modelling of these diseases. |
| Applications |
Optimization: Investigation of metabolic networks by optimization methods such as linear programming, quadratic programming, mixed integer linear programming and genetic algorithm. Statistics: Investigation and interpretation of biological data by several statistical tests Data Mining: Analysis of genome-wide data (transcriptome, proteome, metabolome, flux distributions) with clustering, principal component analysis, and other dimension reduction methods Mathematical Modelling: Developing mathematical models for cell metabolism |
| Projects |
1. TÜBİTAK, Ardeb 1003 (2017-2020), ‘Creation of dormancy models of non-small cell lung carcinoma and investigation of its etiopathogenesis using omics methods’, 2.450.000 TL 2. TÜBİTAK, Ardeb 1001 (2017-2020), ‘Mathematical Modelling and Improvement of Reprogramming and Differentiation Processes of Induced Pluripotent Stem Cells,335.200 TL 3. TÜBİTAK, Ardeb 1003 (2017-2020), “Bioinformatic analysis of transcriptome data and cellular networks for Parkinson’s Disease: Identification of novel drug targets and drugs”, 765.000 TL 4. TÜBİTAK Bideb 2232 (2016-2018), ‘New generation of solutions to biofuel production via reconstruction of metabolic network and carbon assimilation pathways of Eubacterium limosum strains: A systems biology approach’, 30.000 TL 5. TÜBİTAK, Ardeb 1002 (2016), “Improvement and optimization of a novel computational method for the inference of cellular networks from omics data: Application to Stem Cells”, 29.470 TL 6. TÜBİTAK, Ardeb 3501 (2011-2013), “Investigation of the cellular objective behind the metabolic behaviours of the cell by using bottom-up and top-down approaches of systems biology in an integrative manner: applications to the metabolisms of microorganisms and human”, 110.000 TL 7. GTÜ, BAP, (2015-2017), “Reconstruction of a new genome-scale metabolic network for the characterization of brain metabolism and application to brain tumors”, 4.800 TL 8. GTÜ, BAP, (2011-2013), “Investigation of the Effect of Neurological Diseases on Brain Metabolism by Using Computational Systems Biology Approaches”, 7.500 TL |
