Prof. Jon Timmis  BSc (Hons), PGCHE, Ph.D., Senior MIEEE

Pro-Vice-Chancellor for Partnerships and Knowledge Exchange

Professor of Intelligent and Adaptive Systems

Tel: +44 (0)1904 32 2318
Fax: +44 (0)1904 32 2335

Research Area: Intelligent Systems and Nano-science Group

Areas of Expertise: Artificial Immune Systems, Computational Immunology, Fault-Tolerant Swarm Robotic Systems.



I am Professor of Intelligent and Adaptive Systems in the Department of Electronic Engineering at the University of York and I am a member of the Intelligent Systems and Nano-science group. I currently hold the position of Pro-Vice-Chancellor for Partnerships and Knowledge Exchange at the University, however I still run an active research lab.

My research cuts across many areas, but most of my work revolves around immunology, either developing computational models of immune function (computational immunology), or fault-tolerance achieved via bio-inspired engineering with a focus on the immune system (immuno-engineering). In terms of applications, I focus mainly on swarm robotic systems as a platform for testing ideas relating to fault tolerance and anomaly detection. My wider interests are in modelling and simulation of complex systems.

I studied Computer Science in the Department of Computer Science, Aberystwyth University and studied for my PhD in the same department in the area of artificial immune systems.  I moved to the University of Kent in 2000 as a Lecturer, then Senior Lecturer at the School of Computing at the University of Kent.  I moved to York in 2005 to take up a position of Reader in a joint appointment between the Departments of Computer Science and Electronic Engineering.  In 2008 I was promoted to Professor (personal chair) and since August 2013 I hold a full-time position in the Department of Electronic Enginering.

I held a Royal Society-Wolfson Research Merit Award (April 2011 - March 2016) which allowed me to focus on developing my work on computational immunology and self-healing swarm robotic systems. For fun, we made a video, of our flying robots (make sure the volume is turned up).  

I was a Royal Academy of Engineering Enterprise Fellow (March 2014 - September 2015) which allowed me time to commericalise our work on supporting evidence-based decision making through computational modelling.  We spun out a company, SimOmics, of which I am currently CEO.  

View my profile on Research Gate or my profile on Google Scholar. For those of you interested in statistics, I have over 12,500 citations and a H-index of 47 (Google Scholar).





Publications information is available via the York Research Database


Current Research Council Projects

ARE: Autonomous Robotic Evolution. Four year project led by Prof Andy Tyrrell with Prof Emma Hart (Napier) and Prof Alan Winfield (Bristol Robotics Lab). EPSRC funded (June 2018 – May 2022)

RoboTest: Systematic Model-Based Testing and Simulation of Mobile Autonomous Robots. Five year project led by Prof Ana Cavalcanti in Computer Science, in collaboration with Prof Jim Woodcock also in Computer Science at York, Prof Rob Hierons and Dr Brijesh Dongo (Brunel). EPSRC funded (April 2018 – March 2023)

Self-repairing Hardware Paradigms based on Astrocte-neuron Models. Four year project led by Dr David Halliday at York, in collaboration with Ulster University and Prof Andy Tyrrell at York. EPSRC funded (Oct 2015 – Sept 2019).

RoboCalc: A Calculus for Software Engineering of Mobile Autonomous Robotics. Five year project led by Prof Ana Cavalcanti in Computer Science, in collaboration with Prof Jim Woodcock also in Computer Science at York,. EPSRC funded (Oct 2015 – Sept 2020).

Bioinspired and Adaptive Architectures. A platform grant from the EPSRC to support work in the Intelligent Systems Group. The grant is led by Prof Andy Tyrrell. (2013 - 2018)

Current Industrial Funding

I am CI on a one PhD CASE awards with the BBSRC and GSK.

I am PI on an InnovateUK funded project for Health and Life Sciences Modelling Infrastructure.

Research Team

Below is a current list of people, that in one way or another, work with me.

Dr Kieran Alden. Kieran is a senior postdoc in my group and is interested in developing novel modelling tools and methods, and helps me look after the whole group.

Computational Immunology

I work extensively with experimental immunologists in the Center for Immunology and Infection here at York and all my computational modelling work is done with a combination of experimental (wet-lab) and modelling approaches.

See York Computational Immunology Laboratory for more information on this area and the people.

Paul Buckley (Computational modelling of infectious disease and associated vaccines) - Co-supervised with Prof Mark Coles (Oxford)

Jonathan Hamp (Mathematical Modelling of Leishmania) - Co-supervised with Prof Paul Kaye (CII) and Prof Simon Croft (LSHTM) 

Bio-Inspired Engineering

Our robot lab is supported by a full-time technician, Dr James Hilder. The vast majority of my work now focusses on fault tolerance issues in collective/swarm robotic systems, and their application to environmental monitoring. We work on aspects from detection, diagnosis and recovery of faults and then emergence of fault tolerance in swarms. Many of our approaches focus on how the immune system can be used as inspiration, so called Artificial Immune Systems (AIS).

Current PhD Students and Postdocs

Dr. Wei Li (Formal methods for robotic controllers) EPSRC funded - Post Doc

Edgar Burumen (Evolution of tasks partitions in swarm robotics) -  Co-supervised with Dr Andy Pomfret (Electronic Engineering)

Naomi Gildert (Investigating implicit and explicit communication in cooperation between humanoid robots.) - Co-supervised with Dr Andy Pomfret (Electronic Engineering)

James O’Keeffe (Evolution of immunity in robotic swarms) -  Co-supervised with Dr Danesh Tarapore (Southampton) and Dr Alan Millard (Electronic Engineering)

Oyinlola Oladiran (Evolution of immunity in robotic swarms) -  Co-supervised with Dr Danesh Tarapore (Southampton) and Dr Alan Millard (Electronic Engineering)

Richard Redpath (Distributed decision making in robotic swarms) - Co-supervised with Dr Martin Trefzer (Electronic Engineering)

James Wilson (Mapping of environments with robotic swarms)  - Co-supervised with Prof Andy Tyrrell (Electronic Engineering)

Guangsha Xu (Mapping of hazardous environments with mobile robots) - Co-supervised with Dr Martin Trefzer (Electronic Engineering)

PhD students awaiting viva

Yuyuan Zhang (Evolving dynamic controllers for robotic systems)  - Co-supervised with Dr Andy Pomfret (Electronic Engineering)

Hoa Wei (Test case generation for robotic swarms) - Co-supervised with Dr Rob Alexander (Computer Science)

Previous Research Students (year of graduation ceremony given)


Jason Cosgrove  The Spatial Distribution and Dynamics of CXCL13 in Lymphoid Tissues. (Biology)


Stephanie Evans. A Computational Approach to Studying the Processes Active During Helicobacter hepaticus-Induced Intestinal Inflammation (Biology)
Alan Millard. Exogenous Fault Detection in Swarm Robotic Systems  (Computer Science)
James Stovold. Distributed Cognition as the Basis for Adaptation and Homeostasis in Robots (Computer Science)
James Butler. Model Hybridisation and Visualisation Techniques for the Investigation of Complex Disease Processes (Biology)


German Leonov.  An integrated molecular cell biology and agent-based simulation approach to dissecting microRNA regulatory networks  (Biology)
Xiaohu Liu. (Electronics) – awaiting final PDF
Paul Taylor. Autonomic Business Processes  (Computer Science)
Anna Ladi. Adaptive Chemical Agent Detection in Dynamic, Changing Environments  (Electronics)


Dr Richard Williams.  An Agent-Based Model of the IL-1 Stimulated Nuclear Factor-kappa B Signalling Pathway (Computer Science)
Dr Dan Moyo. Investigating the Dynamics of Hepatic Inflammation through Simulation. (Computer Science)
Dr NuralHuda Mohd Azmi. Artificial Immune Systems for Information Filtering: Focussing on Profile Adaptation. (Computer Science)


Dr Piero Conco. An Adaptive Framework for Classification of Concept Drift with Limited Supervision. (Electronics)
Dr Lim Tiong Hoo. Dependable Network Protocols in Wireless Sensor Networks. (Computer Science).
Dr Lachlan Murray. Fault Tolerant Morphogenesis in Self-reconfigurable Modular Robotic Systems. (Electronics). Dr Jenny Owens. An Invesitgtion of Loose Coupling in Evolutionary Swarm Robotics. (Computer Science).


Dr. Kieran Alden. Modelling and Simulation of lyphoid tissue organogenesis. (Biology). 2012. Dr. Antonio Zamorano. Complex Systems Simulation, design and implementation using FPGAs. (Electronics). 2012.
Dr. Ran Bi. Immune-inspired fault diagnosis for a robotic system. (Electronics) 2012.
Dr. Lau Hui Keng (Kelvin). Error Detection in Swarm Robotics: A Focus on Adaptivity to Dynamic Environments. (Computer Science) 2012.
Dr. Ameila Ismail (Rita). Immune-inspired Self Healing in Swarm Robotic Systems. (Computer Science) 2012.


Dr. Omer Qadir. Protien Processor Associate Memory. (Electronics) 2011.
Dr Mark Read. Statistical and Modelling Techniques to Build Confidence in the Investigation of Immunology through Agent-Based Simulation. (Computer Science). 2011.
Dr. Richard Greaves. Computational Modelling of Treg Networks in Experimental Autoimmune Encephalomyelitis. (2011) (MSc by Research)


Dr Nick Owens. From Biology to Algorithms. (Electronics). 2010.
Dr Luca Albergante (Milan). A Petri Net Model of Liver Response to Visceral Leishmaniasis: self-regulation and complex interplay in the vertebrate immune system. (Mathematics) 2010.
Dr Adam Knowles Immunologically Inspired Data Fusion for Anomaly Detection in Electromechanical Systems PhD. (Electronics). 2010.
Dr Yang Liu A Neuro-Immune Inspired Computational Framework and its Applications to a Mchine Visual Tracking System PhD. (Electronics) 2010.


Dr Ed Clark A Framework for modelling stochastic optimisation algorithms with Markov chains. PhD. (Electronics) 2009.
Dr Paul Andrews An Investigation oor the Development of Artificial Immune Systems: A Case-Study in Immune Receptor Degeneracy PhD. (Computer Science) 2009. 


Dr. Peter May. An Artficial Immune System Approach to Mutation Testing Test Data Generation PhD. (Computer Science) 2006.
Dr. Andy Secker. Artificial Immune Systems for Web Content Mining: Focusing on the Discovery of Interesting Information PhD. (Computer Science) 2006.


Dr. Modupe Ayara. An Immune Inspired Approach For Adaptable Error Detection in Embedded Systems PhD. (Computer Science) 2005.
Dr. Andrew Watkins. Exploiting Immunological Metaphors in the Development of Serial, Parallel and Distributed Learning Algorithms PhD. (Computer Science) 2005.
Dr. Tom Knight. MARIA: A Multilayered Unsupervised Machine Learning Algorithm Based on the Vertebrate Immune System PhD. (Computer Science) 2005.


Dr Giuseppe Nicosia (Catania, Italy). Immune Algorithms for Optimisation and Protein Structure Prediction, (Mathematics and Computer Science) 2004.
Johnny Kelsey. An Immune Inspired Algorithm for Function Optimisation . MSc by Research (Computer Science). 2004.

Selected Previous Research Projects

CoCoRo. Collective Cognitive Robotics, funded by the EU. We are developing the operating systems and middleware that has inbuilt artificial immune systems, and also developing a swarm-based recovery strategy based on T Regulatory networks.

 Resilent Futures. Complex systems modelling project developing simulations for stakeholders in the transport and energy industries.

Ecosystem Interactions. Funded by DEFRA. Collaboration with Prof Piran White, Dave Raffaelli, Department of Environment and Geography at York, and Prof Stuart Bell, York Law School.



I have done a variety of public engagement activities including:

Edinburgh Science Festival 2015

CBBC Technobabble, episode 8 of the first season, broadcast in Nov/Dec 2014 and also on the iPlayer.  

Royal Society Summer Science Exhibition (schools talks) 2014, read about the event.

Edinburgh Fringe Festival 2013 (Skeptics in the Pub).  Read the overview for more details.

An interview I did with Gusz Eiben in 2012 as part of the AWARNESS co-ordinating action.  Here I talk about artificial immune systems and how we should be evolving them.

I have given a variety of public lectures,  includin one in 2012 that we recorded on "Can a robot have an immune system

I have done a variety of media events, including interviews for ITV, BBC (TV and radio).

Random Videos

My lab made a video of our flying swarm of robots doing quite a cool dance (make sure the volume is turned up)