I am a PhD student working within the CRISP group (a collaboration between Aberdeen University, Exeter University and Imperial College) under the supervision of Professor Stumpf and Professor Haynes. My background is computational, having obtained a BA in Mathematics from the University of Oxford in 2003, and a distinction in the Bioinformatics and Theoretical Systems Biology Masters degree from Imperial College, London in 2009.
I am currently developing computational tools for reverse-engineering and designing systems that exhibit observed or desired dynamical features.
Recent oral presentations
May 2012 – Computational Biology Institute Annual Symposium, University of Cambridge.*
Nov 2011 – 5th Institute of Systems and Synthetic Biology Annual Symposium, Imperial College, London.
Oct 2010 – 4th International Workshop on Machine Learning in Systems Biology, University of Edinburgh.
Mar 2010 – 20th Workshop on Mathematical and Statistical Aspects of Molecular Biology, University of Warwick.
- Silk, Kirk, Barnes, Toni, Rose, Moon, Dallman, Stumpf (2011), Designing attractive models: automated identification of chaotic and oscillatory dynamical regimes, Nature Communications, 2:489.
- Barnes†, Silk†, Stumpf (2011), Bayesian design strategies for synthetic biology, Interface Focus, 1:995-908.
- Barnes, Silk, Sheng, Stumpf (2011), Bayesian design of biological systems, Proc Natl Acad Sci USA, 108:15190-15195.
- Kaloriti, Tillmann, Cook, Jacobsen, You, Lenardon, Ames, Barahona, Chandrasekaran, Coghill, Goodman, Gow, Grebogi, Ho, Ingram, McDonagh, de Moura, Pang, Puttnam, Radmaneshfar, Romano, Silk, Stark, Stumpf, Thiel, Thorne, Usher, Yin, Haynes, Brown (2012), Combinatorial stresses kill pathogenic Candida species, Medical Mycology.
- Silk†, Filippi†, Stumpf (2013), Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems, Statistical Applications in Genetics and Molecular Biology, 12:5:603–618.
†These authors contributed equally to the study.
- Silk, Kirk, Barnes, Stumpf 2010, Automated detection of chaotic and oscillatory regimes, Proceedings of the Fourth International Workshop on Machine Learning in Systems Biology, pp. 59-66.