Jonathan Blakes

PhD student and researcher

Interdisciplinary Computing and Complex Systems (ICO2S) research group

Research

I am researching executable biology formalisms (particularly P systems) and developing software tools for modelling natural and synthetic biological systems. Our project is titled Infobiotics and is funded by the EPSRC.

P systems, computing with membranes, abstract the structure and function of the living cell into a formalism upon which we are building an integrated modelling environment for multi-scale systems biology models. We execute P system models of quorum sensing in the bacterial pathogen Pseudomonas aeruginosa and root development in Arabidopsis thaliana using exact stochastic simulation algorithms to obtain trajectories of the systems behaviour in terms of molecular quantities. We can visualize the changes in these quantities in time and space to gain an intuitive understanding the systems dynamics.

Previously (during my MSc in 2006) I developed a Java application for the analysis of DNA walks - 2D representations of chromosome-length nucleotide sequences - and pretensiously named it Icarus. The Icarus website, from which you can launch Icarus using Java WebStart and read my MSc dissertation and PowerPoint presentation, is mirrored here.

Publications

Journal Papers

1. Blakes J, Twycross J, Romero-Campero FJ and Krasnogor N. "The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology" Bioinformatics 2011 [DOI (open access),documentation]

Conference Papers

1. Romero-Campero FJ, Twycross J, Cao H, Blakes J, Krasnogor N. "A Multiscale Modelling Framework Based On P Systems" Workshop on Membrane Computing 2008 (WMC9) Edinburgh, UK, July 28-31, Revised Selected and Invited Papers in Lecture Notes in Computer Science 5391: 63-77. [pdf]

2. Smaldon J, Blakes J, Lancet D, Krasnogor N. "A Multi-scaled Approach to Artificial Life Simulation With P Systems and Dissipative Particle Dynamics" Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2008 Atlanta, USA), 249-256, ACM Publisher, 2008. [pdf,bibtex]

Extended Abstracts

1. Blakes J, Krasnogor N, Romero-Campero FJ, Twycross J. "An Executable Biology Methodology for Systems and Synthetic Biology" Proceedings of the ECCB Satellite Meeting on Probabilistic Modelling in Computational Biology, Cagliari, Sardinia, September 2008. [pdf]

Posters

1. Blakes J, Romero-Campero FJ, Twycross J, Cao H, Krasnogor N. "An Integrated Development Environment for Synthetic Biology Models" presented at European Conference on Synthetic Biology (ECSB) II: Design, Programming and Optimisation of Biological Systems (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 29 March - 03 April 2009. [pptx,pdf]

2. Romero-Campero FJ, Blakes J, Camara M, Krasnogor N. "A systems analysis of the AHL Quorum Sensing system in Pseudomonas aeruginosa" presented at Systems Biology (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 12-17 April 2008. [ppt]

3. Romero-Campero FJ, Blakes J, Cao H, Camara M, Krasnogor N. "A modular and stochastic approach to the study of gene circuits using P systems" presented at Genomes to Systems Manchester, UK March 17-19 2008. [pdf]

4. Romero-Campero FJ, Blakes J, Camara M, Willams P, Perez-Jimenez MJ, Krasnogor N. "Formal informatics and machine learning for more principled systems and synthetic biology" presented at European Conference on Synthetic Biology (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 24-29 November 2007. [pdf]

Photos

The Infobiotics team dining out during the Genomes to Systems conference in Manchester (clockwise from left: Hongqing Cao, James Smaldon, Jonathan Blakes, Jamie Twycross, Fran Romero-Campero).