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 

Gebze Institute of Technology, Department of Bioengineering, 41400,
Gebze-Kocaeli, Turkey 

Web Page

Laboratory Staff

Res. Assist. Gülben Avşar (PhD Student)
M. Jafar Khatibipour (PhD Student)
Res. Assist. Emrah Özcan (PhD Student)
Res. Assist. Şükrü Öztürk (PhD Student)
Res. Assist. Ecehan ABDİK (MSc Student)
Res. Assist. Müberra Fatma Cesur (MSc Student)
Hamza Umut Karakurt (MSc Student)
Ali Kaynar (MSc Student)
Furkan Kurtoğlu (MSc Student)
İsa Yüksel (MSc 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:
  • Neurodegenerative diseases
  • Cancer (non-small cell lung cancer, brain tumor)
  • Stem cells
  • Infectious diseases

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.


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


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

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