Education
PhD in Bioengineering
2012–2018Marmara University, İstanbul
Bioengineering Department, Computational Biology and Bioinformatics Research Group. Grade: 3.93/4.00
Thesis: "Computational Dynamical Characterization of Human Major Histocompatibility Complex Proteins"
MSc in Biotechnology
2008–2011Hamburg University of Technology (TUHH), Germany
Grade: very good (1.5)
Thesis: "Development of a MATLAB-based Tool for Evaluation of Fed-Batch Process Strategies in Mammalian Cell Culture"
ERASMUS Exchange Student
2007Abo Akademi, Turku, Finland
Chemical Engineering
Bachelor of Science, Bioengineering
2003–2008Ege University, İzmir, Turkey
Grade: 79.5/100
Work Experience
Assistant Professor
2020–presentGebze Technical University, Bioengineering Department, Gebze, Kocaeli, Turkey
Deputy Head of Department. Member of Bioinformatics and Systems Biology Graduate Program Executive Committee.
Courses: Bioinformatics Fundamentals, Structural Bioinformatics and Computational Drug Design, Mass and Energy Balances, Fundamentals of Bioengineering
Assistant Professor
2019–2020Recep Tayyip Erdogan University, Bioengineering Department, Rize, Turkey
Deputy Head of Department.
Courses: Introduction to Programming with Python
Research Assistant
2013–2018Marmara University, Bioengineering Department, İstanbul, Turkey
Courses: Mathematical Applications in Bioengineering Systems, Biotransport Phenomena, General Biology for Bioengineers Laboratory, Biochemistry for Bioengineers I/II, Bioengineering Laboratory I/II
Internship
2006Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
Environmental Microbiology Department
Research Projects
Discovery of novel allosteric ERK5 kinase inhibitors using a drug repurposing approach
2022–2023Funded by: Health Institutes of Türkiye | Role: Researcher
Prediction of sub-type specific drug targets and novel drug candidates from transcriptome data: Application to Alzheimer's disease and liver cancer
2022–2023Funded by: GTÜ | Role: Researcher
Systematic characterization of structure and function of HLA-B39 subtypes to decipher their association with autoimmune (Type 1) diabetes
2021–2022Funded by: GTÜ | Role: Joint Coordinator with M. A. Garstka, XJTU
Dynamical Characterization of HLA Proteins
2013–2015Funded by: TÜBİTAK | Role: Scholarship Holder
Publications
For a complete list of publications, please visit the Publications page.
Skills
Languages
English: advanced level (IELTS 8/9, YÖKDİL 100/100) · German: upper-intermediate/advanced level (B2)
Programming
MATLAB (advanced) · Python (advanced) · R (intermediate) · C (beginner) · Javascript (beginner)
Software
VMD, NAMD, Gromacs, ProDy · Autodock and Autodock Vina · Rosetta Suite · Git
Computational Biology
Scientific programming · Molecular modeling and simulation · Molecular dynamics · Molecular docking · GUI development
Wet Lab
Microbiology and light microscopy · Mammalian cell culture · Bioprocess engineering and bioreactor operation · Analytical spectroscopic methods: HPLC, GC-MS · Column chromatography and TLC · Molecular biology methods: electrophoresis, PCR
Awards
TEV/DAAD Germany Master's Scholarship (Scholarship)
IAESTE Scholarship (Internship)