Get to know the Students Committee members: Zeynep Karagoz

TELL US SOMETHING ABOUT YOURSELF!

I am Zeynep, I was born in Turkey and I obtained my bachelor’s degree in molecular biology and genetics in Bogazici University, Istanbul. Then I moved to Munich, Germany for my master studies, where my focus was computational biology and bioinformatics. Currently I am a 3rd year PhD candidate in MERLN Institute for Technology-Inspired Regenerative Medicine in Maastrichty, the Netherlands and I am working on computational modeling of the cell-extracellular matrix interactions.

2. HOW DID YOU FIRST GET INVOLVED WITH THE VPHI? WHAT IS THE MOST SIGNIFICANT ADDED VALUE OF BEING A VPHI STUDENT MEMBER?

My supervisor Dr. Aurélie Carlier who is also a member of the VPHi introduced me to the institute on my first year.

I believe being a student member of the VPHi broadened my perspective about computational modeling and its medical applications. Via the webinars, conferences and especially the summer school, I got to know scientists from different fields and learnt in silico methods that I was not aware of.

3. CAN YOU DESCRIBE YOUR PHD RESEARCH WORK IN 3 SENTENCES?

General theme of my project is about describing how cells react to the changes in their extracellular environment. I focus on modeling the cell decision-making processes, which are affected by the chemical and mechanical cues that come from the extracellular matrix. I am building three different models at three different scales: 1) molecular scale model of cell surface receptor-ligand binding 2) cellular scale model of signaling network crosstalk and its effect on cell proliferation 3) tissue scale model of fibroblast to myofibroblast transition, which is initiated by extracellular matrix tension.

4. WHAT IS THE EXPECTED OUTCOME YOU WOULD LIKE TO ACHIEVE?

With these models, I expect to provide predictions on optimal biomaterial or cell culture system design. For regenerative medicine applications, targeting the cells in the right way to steer cell behavior is very important. Yet we do not have a complete understanding of how the cells interpret the external cues. I would like my models to help solving this puzzle.

5. HAVE YOU ALREADY PUBLISHED ANY PAPERS AS PART OF YOUR RESEARCH WORK? OR HAVE YOU REACHED ANY RESULTS THAT MAKE YOU PROUD?

I have a review article and a research article that were both published in 2021.

• The review of computational models of integrin signaling at 3 subcellular levels and how such models can help biomaterial design: Karagöz, Z., Rijns, L., Dankers, P.Y.W., Griensven, M. v., Carlier, A., (2021) Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks, Computational and Structural Biotechnology Journal, 19: 303-314, https://doi.org/10.1016/j.csbj.2020.12.025.
• The research article where we explore the dynamics of ligand competition for integrin binding: Karagöz Z, Geuens T, LaPointe VLS, van Griensven M and Carlier A (2021) Win, Lose, or Tie: Mathematical Modeling of Ligand Competition at the Cell–Extracellular Matrix Interface. Frontiers in Bioengineering and Biotechnology 9:657244. doi: 10.3389/fbioe.2021.657244