SURE

Article

Li, Wei, Buchanan, Edgar, Le Goff, Léni K., Hart, Emma, Hale, Matthew F., De Carlo, Matteo, Wooley, Robert, Winfield, Alan F., Timmis, Jonathan and Tyrrell, Andy M. (2023) Evaluation of frameworks that combine evolution and learning to design robots in complex morphological spaces. IEEE Transactions on Evolutionary Computation. ISSN 1089-778X (In Press)

Buchanan, Edgar, Alden, Kieran, Pomfret, A, Timmis, Jonathan and Tyrrell, Andy M. (2023) A study of error diversity in robotic swarms for task partitioning in foraging tasks. Frontiers in Robotics and AI, 9. ISSN 2296-9144

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

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

Book Section

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

Book

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