About Me

Hi, I am Ruud, and I just completed a computing science PhD in the ICOS group at Newcastle University. I have a background as a physicist; a master and bachelor degree in Physics at the Universities of Amsterdam (Vrije Universiteit and Universiteit van Amsterdam). However, in my PhD (and previous jobs) I developed myself as a data scientist/software developer.



In my research in the synthetic biology field, I looked at how genetic information's spatial location plays a role in single-cell system dynamics. It is seen that increasing the distance of two parts of a simple pathway can drastically affect its dynamics. When I think of the spatial organisation of the transcribed components, especially small proteins, it seems to me that diffusion on the scale of an E.Coli would cause this organisation to be a short transient process. This would lead to the conclusion that spatial organisation effects are not significant over a protein lifetime. These conflicting observations attracted me to find what is causing this dissonance of this initial model and experiment. I have developed a model consolidating these observations using mathematics and data science, as seen in the publications below.



Our team

Ruud Stoof

Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group
School of Computing Science
Urban Science Building (USB)
Newcastle University
Newcastle upon Tyne