My academic interests lie in the branch of computer science that concerns formal languages and their applications. I am particularly excited about formal languages in the context of biology, where my aim is to further our understanding of complex biological processes and ultimately exploit this understanding in the development of novel drug therapies.
My PhD is supervised by Gordon Plotkin and funded by Microsoft Research , and involves the design of two formal languages. The first, named the "Language for Biochemical Systems" (LBS), allows the modelling of cellular signalling pathways in a natural and modular manner. Models in LBS can be translated to a variety of mathematical objects for subsequent analysis and simulation. The second is a language for "Genetic Engineering of living Cells" (GEC) which allows synthetic gene circuits to be designed at a high level of abstraction and subsequently translated to actual sequences of DNA. GEC is developed in collaboration with Andrew Phillips . Prototype tools for both languages are available here. My thesis is here.
Before starting my PhD I studied computer science at Aalborg University . My master's thesis on logics for the Applied Pi calculus, supervised by Hans Hüttel, can be found here .
My CV is here and a list of (peer-reviewed) publications follows below.
- A language for biochemical systems: design and formal specification (with Gordon Plotkin), To appear in TCSB (pdf).
- Towards programming languages for genetic engineering of living cells (with Andrew Phillips), J. R. S. Interface, 2009 (open access).
- A language for biochemical systems (with Gordon Plotkin), Proc. CMSB 2008 (pdf).
- Compositional definitions of minimal flows in Petri nets, Proc. CMSB 2008 (pdf).
- A logical characterisation of static equivalence (with Hans Hüttel), Proc. MFPS 2007 (pdf).