Part Time
Department of Chemical Engineering, Boğaziçi University, Bebek 34342, Istanbul-TURKEY
+90 (212) 359 7126

PhD: Biochemistry, University of Paris VII, CNRS, Molecular Genetics Center, France, 1977
MS: Chemical Engineering, Istanbul University, Turkey, 1972
BS: Chemical Engineering, Istanbul University, Turkey, 1970



Honors and Awards: 

- Bogazici University, Excellence in Science Award, 2008

Research Interests: 
  • Determination of rational design strategies to construct industrially important microorganisms by using systems biology approaches
  • Improvement of biological processes via metabolic engineering approaches
  • Identification of functional modules in yeast and humans with an ultimate goal of understanding multifactorial diseases
  • Reconstruction and analysis of biological networks to understand the mechanism behind the cellular processes Integration and analysis of different omics data
Selected Papers: 
  • 1. HerrgÂrd MJ., Swainston N., Dobson P., Dunn WB., Arga KY., Arvas M., Blüthgen N., Borger S., Costenoble R., Heinemann M., Hucka M., Le NovËre N., Li P., Liebermeister W., Mo ML., Oliveira AP., Petranovic D., Pettifer S., Simeonidis E., Smallbone K., Spasic I., Weichart D., Brent R., Broomhead DS., Westerhoff HV., Kirdar B., Penttila M., Klipp E., Palsson Bÿ., Sauer U., Oliver, SG., Mendes P., Nielsen J., Kell DB., 2008. A consensus yeast metabolic network obtained from a community approach to systems biology, Nature Biotechnology, 26, 1155-60.
  • 2. Cakır T., Patil KR., Onsan ZÜ., Ulgen KO., Kirdar B., Nielsen J., 2006. Integration of mtabolome data with metabolic networks reveals reporter reactions, Molecular Systems Biology, 2:50.
  • 3. Pir P., Ulgen KO., Hayes A., Onsan ZI., Kirdar B., Oliver SG., 2006. Integrative Investigation of Metabolic and Transcriptomic Data, BMC Bioinformatics, 7:203.
  • 4. Cakir T, B. Kırdar, Ülgen K, 2004. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks, Biotechnology and Bioengineering 86(3), 251-60.
  • 5. Birol G., Onsan ZI., Kırdar B., Oliver SG., 1998, Ethanol production and fermentation characteristics of recombinant Saccharomyces cerevisiae strains grown on starch, Enzyme and Microbiol Technology, 22, 672-7.
Research Laboratory: 
Biosystems Engineering Research Group