Deputy Vice-Chancellor (Commercial)
I am Professor in Intelligent and Adaptive Systems in the School of Computer Science and Deputy Vice-Chancellor (Commercial) at the University.
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.
I then 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 from August 2013, I was full-time in the Department of Electronic Engineering. I was Head of Department from 2015 to 2017 and then Pro-Vice-Chancellor (Partnerships and Knowledge Exchange) from 2017 to 2019 before joining Sunderland as Deputy Vice-Chancellor.
My research is interdisciplinary and cuts across areas of computational biology (with a focus on immunology), robotics (with a focus on swarm and evolutionary robotics) and fault-tolerance achieved via bio-inspired engineering. My wider interests are in modelling and simulation of complex systems.
I held a Royal Society-Wolfson Research Merit Award (2011 to 2016) which allowed me to focus on developing my work on computational immunology and self-healing swarm robotic systems.
I was a Royal Academy of Engineering Enterprise Fellow (2014 - 2015) which allowed me time to commercialise our work on supporting evidence-based decision making through computational modelling. We spun out a company, Simomics, in 2014, where I currently serve as CTO.
Le Goff, Léni K., Buchanan, Edgar, Hart, Emma, Eiben, Agoston E., Li, Wei, De Carlo, Matteo, Winfield, Alan F., Hale, Matthew F., Wooley, Robert, Angus, Mike, Timmis, Jonathan and Tyrrell, Andy M. (2022) Morpho-evolution with learning using a controller archive as an inheritance mechanism. IEEE Transactions on Cognitive and Developmental Systems. ISSN 2379-8939
Cosgrove, Jason, Alden, Kieran, Stein, Jens, Coles, Mark and Timmis, Jonathan (2021) Simulating CXCR5 Dynamics in Complex Tissue Microenvironments. Frontiers in Immunology. ISSN 1664-3224
Wooley, Robert, Timmis, Jonathan and Tyrrell, A.M. (2021) Cylindabot: Transformable Wheg Robot Traversing Stepped and Sloped Environments. Robotics, 10 (3). ISSN 2218-6581
Woolley, Robert, Timmis, Jon and Tyrrell, Andy M. (2021) Cylindabot: Transformable Wheg Robot Traversing Stepped and Sloped Environments. Robotics, 10 (3). e104. ISSN 2218-6581
Buchanan, Edgar, Le Goff, Léni K., Li, Wei, Hart, Emma, Eiben, Agoston E., De Carlo, Matteo, Winfield, Alan F., Hale, Matthew F., Woolley, Robert, Angus, Mike, Timmis, Jon and Tyrrell, Andy M. (2020) Bootstrapping Artificial Evolution to Design Robots for Autonomous Fabrication. Robotics, 9 (4). e106. ISSN 2218-6581
Cosgrove, Jason, Novkovic, Mario, Pikor, Natalia, Zhou, Zhaokun, Onder, Lucas, Morbe, Urs, Cupovic, Jovana, Miller, Helen, Alden, Kieran, Thuery, Anne, O-Toole, Peter, Jarrett, Simon, Taylor, Emily, Venetz, Daniel, Heller, Manfred, Uguccioni, Mariagrazia, Legler, Daniel, Lacey, Charles, Coatesworth, Andrew, Polak, Wojciech, Cupedo, Tom, Manoury, Benedicte, Thelen, Marcus, Sten, Jen, Wolf, Marlene, Leake, Mark, Timmis, Jonathan, Ludewig, Berkhard and Coles, Mark (2020) B-cell Zone Reticular Cell Microenvironments Shape CXCL13 Gradient Formation. Nature Communications, 11. p. 3677. ISSN 2041-1723
Read, Mark, Alden, Kieran, Andrews, Paul and Timmis, Jonathan (2020) Strategies for calibrating models of biology. Briefings in Bioinformatics, 21 (1). pp. 24-35. ISSN 1467-5463
Forrester, S, Siefert, K, Ashwin, H, Brown, N, Zelmar, A, James, S, Lagos, D, Timmis, Jonathan, Chatterjee, M, Mottram, JC, Croft, SL and Kaye, PM (2019) Tissue-specific transcriptomic changes associated with AmBisome® treatment of BALB/c mice with experimental visceral leishmaniasis version 1; peer review: 3 approved. Wellcome Open Research, 4 (198). ISSN 2398-502X
Tarapore, Danesh, Timmis, Jonathan and Christensen, Anders Lyhne (2019) Fault Detection in a Swarm of Physical Robots Based on Behavioral Outlier Detection. IEEE Transactions on Robotics, 35 (6). pp. 1516-1522. ISSN 1552-3098
Buckley, Paul R., Alden, Kieran, Coccia, Margherita, Chalon, Aurélie, Collignon, Catherine, Temmerman, Stéphane T., Didierlaurent, Arnaud M., van der Most, Robbert, Timmis, Jonathan, Andersen, Claus A. and Coles, Mark C. (2019) Application of Modeling Approaches to Explore Vaccine Adjuvant Mode-of-Action. Frontiers in Immunology, 10. ISSN 1664-3224
Wilson, James, Timmis, Jonathan and Tyrrell, Andy (2019) An Amalgamation of Hormone Inspired Arbitration Systems for Application in Robot Swarms. Applied Sciences, 9 (17). e3524. ISSN 2076-3417
Liu, Junxiu, McDaid, Liam, Araque, Alfonso, Wade, John, Harkin, Jim, Karim, Shvan, Henshall, David C., Connolly, Niamh M. C., Johnson, Anju P., Tyrrell, Andy M., Timmis, Jonathan, Millard, Alan G., Hilder, James and Halliday, David M. (2019) GABA Regulation of Burst Firing in Hippocampal Astrocyte Neural Circuit: A Biophysical Model. Frontiers in Cellular Neuroscience, 13. p. 335. ISSN 1662-5102
Cucurull-Sanchez, Lourdes, Chappell, Michael J., Chelliah, Vijayalakshmi, Amy Cheung, S. Y., Derks, Gianne, Penney, Mark, Phipps, Alex, Malik-Sheriff, Rahuman S., Timmis, Jonathan, Tindall, Marcus J., van der Graaf, Piet H., Vicini, Paolo and Yates, James W. T. (2019) Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. CPT: Pharmacometrics & Systems Pharmacology, 8 (5). pp. 259-272.
Miyazawa, Alvero, Ribero, Pedro, Cavalcanti, Anna, Timmis, Jonathan and Woodcock, Jim (2019) RoboChart: modelling and verification of the functional behaviour of robotic applications. Software Systems and Modelling, 18. pp. 3097-3149.
O'Keeffe, James, Tarapore, Danesh, Millard, Alan G. and Timmis, Jonathan (2018) Adaptive Online Fault Diagnosis in Autonomous Robot Swarms. Frontiers in Robotics and AI, 5. p. 131.
Liu, Junxiu, McDaid, Liam, Harkin, Jim, Karim, Shvan, Johnson, Alan Gregoryand Hilder, Millard, Alan, Tyrrell, Andy and Timmis, Jonathan (2018) Exploring Self Repair in a Coupled Spiking Astrocyte Neural Network. IEEE Transactions on Neural Networks and Learning Systems.
Alden, Kieran, Cosgrove, Jason, Coles, Mark and Timmis, Jonathan (2018) Using Emulation to Engineer and Understand Simulations of Biological Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. ISSN 1545-5963
Johnson, Anju P, Junxiu, Liu, Millard, Alan G, Shvan, Karim, Tyrrel, Andy M, Harkin, Jim, Timmis, Jonathan, McDaid, Liam J and Halliday, David M (2017) Homeostatic Fault Tolerance in Spiking Neural Networks: A Dynamic Hardware Perspective. IEEE Transactions on Circuits and Systems, 65 (2). pp. 687-689. ISSN 1549-8328
Ribba, B., Grimm, H. P., Agoram, B., Davies, M. R., Gadkar, K., Niederer, S., van Riel, N., Timmis, Jonathan and van der Graaf, P. H. (2017) Methodologies for Quantitative Systems Pharmacology (QSP) Models: Design and Estimation. CPT: pharmacometrics & systems pharmacology.
Karim, S., Harkin, J., McDaid, L., Gardiner, B., Liu, J., Halliday, D.M., Tyrrell, A.M., Timmis, Jonathan, Millard, A. and Johnson, A. (2017) Assessing Self-Repair on FPGAs with Biologically Realistic Astrocyte-Neuron Networks. IEEE Computer Society Annual Symposium on VLSI, ISVLSI, 2017-J. pp. 421-426. ISSN 2159-3477
Evans, Stephanie, Alden, Kieran, Cucurull-Sanchez, Lourdes, Larminie, Christopher, Coles, Mark C, Kullberg, Marika C and Timmis, Jonathan (2017) ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behavior. PLOS Computational Biology, 13 (2). ISSN 1553-734X
Tarapore, Tarapore, Christensen, Anders Lyhne and Timmis, Jonathan (2017) Generic, scalable and decentralized fault detection for robot swarms. PLOS One. ISSN 1932-6203
Timmis, Jonathan, Alden, K, Andrews, P, Clark, E, Nellis, A, Naylor, B, Coles, M and Kaye, P (2016) Building confidence in quantitative systems pharmacology models: An engineer's guide to exploring the rationale in model design and development. CPT: Pharmacometrics & Systems Pharmacology. ISSN 2163-8306
Read, Mark M, Bailey, Jacqueline, Timmis, Jonathan and Chtanova, Tatyana (2016) Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection. PLOS Computational Biology, 12 (9). ISSN 1553-734X
Read, Mark N, Alden, Kieran, Rose, Lois M and Timmis, Jonathan (2016) Automated Multi-Objective Calibration of Biological Agent-Based Simulations. Journal of the Royal Society Interface, 13 (122). ISSN 1742-5689
Alden, Kieran, Timmis, Jonathan, Andrews, Paul. S, Veiga-Fernandes, Henrique and Coles, Mark C. (2016) Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 (2). pp. 431-442. ISSN 1545-5963
Alden, Kieran James, Andrews, Paul Simon, Polack, Fiona, Veiga-Fernandes, Henrique, Coles, Mark Christopher and Timmis, Jonathan (2015) Using argument notation to engineer biological simulations with increased confidence. Journal of the Royal Society Interface, 12 (104). ISSN 1742-5689
Patel, Amisha, Harker, Nicola, Moreira-Santos, Lara, Ferreira, Manuela, Alden, Keiran, Timmis, Jonathan, Foster, Katie, Garefalaki, Anna, Pachnis, Vassilis, Andrews, Paul, Enomoto, Hideki, Milbrandt, Jeffrey and Veiga-Fernandes, Henrique (2012) Differential RET signaling pathways drive development of the enteric lymphoid and nervous systems. Science signaling, 5 (235). ISSN 1945-0877
Hale, Matthew F., Angus, Mike, Buchanan, Edgar, Li, Wei, Woolley, Robert, Le Goff, Léni K., De Carlo, Matteo, Timmis, Jonathan, Winfield, Alan F., Hart, Emma, Eiben, Agoston E. and Tyrrell, Andy M. (2021) Hardware Design for Autonomous Robot Evolution. In: IEEE Symposium Series on Computational Intelligence. IEEE. ISBN 9781728125473
Buchanan, Edgar, Le Goff, Léni K., Hart, Emma, Eiben, Agoston E., De Carlo, Matteo, Li, Wei, Hale, Matthew F., Woolley, Robert, Timmis, Jonathan and Tyrrell, Andy M. (2020) Evolution of Diverse, Manufacturable Robot Body Plans. In: 2020 IEEE Symposium Series on Computational Intelligence (SSCI). IEEE. ISBN 9781728125473
Johnson, A.P., Halliday, D.M., Millard, A.G., Tyrrell, A.M., Timmis, Jonathan, Liu, J., Harkin, J., McDaid, L. and Karim, S. (2017) An FPGA-based hardware-efficient fault-tolerant astrocyte-neuron network. In: 2016 IEEE Symposium Series on Computational Intelligence (SSCI). UNSPECIFIED. ISBN 9781509042401
Cavalcanti, Ana, Dongol, Brijesh, Hierons, Rob, Timmis, Jonathan and Woodcock, Jim (2021) Software Engineering for Robotics. Springer. ISBN 9783030664947
Stepney, Susan, Pollack, Fiona, Alden, Kieran, Andrews, Paul, Bown, James, Droop, Alistair, Greaves, Richard, Read, Mark, Sampson, Adam, Timmis, Jonathan and Winfield, Alan (2019) Engineering Simulations as Scientific Instruments: A Pattern Language. Springer. ISBN 9783030019389
- Computational and mathematical biology
- Swarm robotics
- Evolutionary computing and robotics
- Fault tolerance
- Anomaly detection
- Artificial Intelligence