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. I was also involved in research on metabolic modeling of red blood cell and brain (neuron & astrocyte) metabolisms during my PhD as a side work.

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) was supported by Netherlands Metabolomics Centre (NMC). Within this context, I worked on the inference of underlying metabolic network structures from metabolome data.

As of May 2011, I am leading the CBS 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 November 2013. I act as a reviewer, among others, for journals Bioinformatics, Molecular Biosystems, Nucleic Acid Research.

I am an advisory board member of the journal Molecular Biosystems, 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).

Research Areas

I aim to conduct a metabolism-centered systems biology research to uncover cellular principles by use of computational techniques.

I work on both top-down (network inference) and bottom-up (flux analysis) sides of Computational Systems Biology area. Microorganism metabolisms (eg. yeast) as well as mammalian metabolisms (eg. brain) are of my interest.

I am also actively involved in the development of a pathogen-host protein-protein interaction database: PHISTO.

Research Projects


Selected Publications

For a full list of publications, see PUBLICATIONS page.