research

September 17th, 2009

I completed my PhD in computing science at Newcastle University in April 2009. My thesis addressed the problem of modelling and analysing genetic regulatory networks; extracting information from them which is commensurate with the current data climate.

Such natural systems are incredibly complex and simply cannot be interpreted by hand, and so there is a real requirement for automated formal techniques. My work centered around exploiting Petri nets, a well-understood formal framework with a substantial tool base which have been applied to many problems in computing science, manufacturing systems and even chemistry. In particular, I devised a suite of qualitative techniques and tools based on Petri nets for modelling, analysing and refining genetic regulatory networks automatically, thus providing much-needed support to the biological community.

 

additional research interests

I am interested in a number of additional research areas, including:

  • model checking and refinement techniques;
  • artificial intelligence;
  • formal methods;
  • process mining
  • cloud computing.

 

publications

Below is a list of my selected publications.

Book Chapters:
  • Banks, R., Khomenko, V. and Steggles, L.J. (2010 exp) Modelling Genetic Regulatory Networks, In Modelling in Systems Biology – the Petri Net Approach, Koch, I. (ed.), Springer.
Journal Papers:
  • Banks, R., Khomenko, V. and Steggles, L.J. (2009) A Case for Using Signal Transition Graphs for Analysing and Refining Genetic Networks, Electronic Notes in Theoretical Computer Science, Vol. 227, pp 3-19. pdf
  • Banks, R. and Steggles, L.J. (2007) A High-Level Petri Net Framework for Genetic Regulatory Networks, Journal of Integrative Bioinformatics, Vol. 4, Issue 3, pp 1-12. pdf
  • Steggles L.J. , Banks, R. , Shaw O. and Wipat, A. (2007) Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach, Bioinformatics, Vol. 23, Issue 3, pp 336-343. pdf
Conference Papers
  • Banks, R., Khomenko, V. and Steggles, L.J. (2008) A Case for Using Signal Transition Graphs for Analysing and Refining Genetic Networks, In 2nd International Meeting on Membrane Computing and Biologically Inspired Process Calculi, MeCBIC 2008, Iasi, Romania, Ciobanu, G. (ed.), pp 38-52.
  • Steggles, L.J., Banks, R. and Wipat, A. (2006) Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets, In Computational Methods in Systems Biology, International Conference, CMSB 2006, Trento, Italy, Priami, C. (ed.), Lecture Notes in Bioinformatics, Vol. 4210, pp 127-141. pdf
Thesis
  • Banks, R. (2009) Qualitatively Modelling Genetic Regulatory Networks: Petri Net Techniques and Tools, School of Computing Science, University of Newcastle upon Tyne. pdf
Posters
  • Banks, R. and Steggles, L.J. (2007) A High-Level Petri Net Framework for Genetic Regulatory Networks,Computational Methods in Systems Biology, International Conference, CMSB 2007, Edinburgh, UK. pdf
  • Banks, R. and Steggles, L.J., Shaw, O. and Wipat, A. (2006) Qualitatively Modelling Genetic Regulatory Networks using Petri Nets: a Case Study of Sporulation in B.subtilis,Systems Biology Workshop, Newcastle University, UK. pdf
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