Computational Systems Biology Group

Department of Bioengineering, Gebze Technical University, TURKEY

Tunahan Çakır, Group Leader

Associate Professor

Gebze Technical University Tunahan Cakir
Detailed CV
Department of Bioengineering
Computational Systems Biology Group
Mail: tcakir [at]
Room: Bioengineering Building, 146
Phone: +90 262 605 33 20


I have received my B.Sc, M.Sc and Ph.D degrees from Department of Chemical Engineering at Bogazici University, Istanbul. My PhD thesis research mainly involved integrative analysis of omics data (metabolomics and transcriptomics) and metabolic networks, and it was partly a collaborative project with Prof. Jens Nielsen. For my post-doctoral project at the Biosystems Data Analysis Group (University of Amsterdam) and at the Department of Metabolic and Endocrine Diseases (University Medical Center Utrecht), I worked on the inference of underlying metabolic network structures from metabolome data.

Currently, I am a group leader in Computational Systems Biology group at Department of Bioengineering in Gebze Technical University, TURKEY. I am one of the co-founders of the start-up company PHI Tech Bioinformatics since 2013. I act as a reviewer, among others, for journals Bioinformatics, Molecular Omics, Plos Computational Biology. I am an advisory board member of the journal Molecular Omics, published by Royal Society of Chemistry, as of September 2015. I am a recipient of 2015 GEBIP (Young Scientist Outstanding Achievement Award) award by Turkish Academy of Sciences (TUBA) and and Research Incentive Award by METU Prof. Mustafa Parlar Foundation (2017).

Research Areas

My research focuses on mapping genome-wide omics data on molecular interaction networks (protein protein interaction networks, genome scale metabolic networks) using computational systems biology methods to elucidate molecular mechanisms of neurodegenerative diseases (Alzheimer's Disease, Parkinson's Disease), infectious diseases and cancer. To this aim, we apply a number of bioinformatics methods to predict potential biomarkers, drug targets and drugs for those diseases. Our main interest is to map disease-associated transcriptome data on molecular interaction networks to shed light on molecular & metabolic mechanisms.

Ongoing Research Projects


Selected Publications

For a full list of publications, see PUBLICATIONS page.