| Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems K Alden, M Read, J Timmis, PS Andrews, H Veiga-Fernandes, M Coles PLoS computational biology 9 (2), e1002916, 2013 | 127 | 2013 |
| Differential RET signaling pathways drive development of the enteric lymphoid and nervous systems A Patel, N Harker, L Moreira-Santos, M Ferreira, K Alden, J Timmis, ... Science signaling 5 (235), ra55-ra55, 2012 | 97* | 2012 |
| B cell zone reticular cell microenvironments shape CXCL13 gradient formation J Cosgrove, M Novkovic, S Albrecht, NB Pikor, Z Zhou, L Onder, U Mörbe, ... Nature communications 11 (1), 3677, 2020 | 74 | 2020 |
| Agent‐based modeling in systems pharmacology J Cosgrove, J Butler, K Alden, M Read, V Kumar, L Cucurull‐Sanchez, ... CPT: pharmacometrics & systems pharmacology 4 (11), 615-629, 2015 | 64 | 2015 |
| Engineering Simulations as Scientific Instruments: A Pattern Language: With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T … S Stepney, FAC Polack Springer, 2018 | 42 | 2018 |
| Pairing experimentation and computational modeling to understand the role of tissue inducer cells in the development of lymphoid organs K Alden, J Timmis, PS Andrews, H Veiga-Fernandes, MC Coles Frontiers in immunology 3, 172, 2012 | 38 | 2012 |
| Strategies for calibrating models of biology MN Read, K Alden, J Timmis, PS Andrews Briefings in Bioinformatics 21 (1), 24-35, 2020 | 27 | 2020 |
| Using argument notation to engineer biological simulations with increased confidence K Alden, PS Andrews, FAC Polack, H Veiga-Fernandes, MC Coles, ... Journal of the Royal Society Interface 12 (104), 20141059, 2015 | 26 | 2015 |
| Automated multi-objective calibration of biological agent-based simulations MN Read, K Alden, LM Rose, J Timmis Journal of the Royal Society Interface 13 (122), 20160543, 2016 | 22 | 2016 |
| Using emulation to engineer and understand simulations of biological systems K Alden, J Cosgrove, M Coles, J Timmis IEEE/ACM transactions on Computational Biology and Bioinformatics 17 (1 …, 2018 | 21 | 2018 |
| dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment K Alden, S Veretnik, PE Bourne BMC bioinformatics 11, 1-7, 2010 | 17 | 2010 |
| Easing parameter sensitivity analysis of NetLogo simulations using SPARTAN K Alden, J Timmis, M Coles Artificial Life Conference Proceedings, 622-628, 2014 | 14 | 2014 |
| Applying spartan to Understand Parameter Uncertainty in Simulations. K Alden, M Read, PS Andrews, J Timmis, M Coles R Journal 6 (2), 2014 | 12 | 2014 |
| Scientific software needs quality control K Alden, M Read Nature 502 (7472), 448-448, 2013 | 12 | 2013 |
| Simulation and statistical techniques to explore lymphoid tissue organogenesis K Alden University of York, 2012 | 12 | 2012 |
| Extending and applying Spartan to perform temporal sensitivity analyses for predicting changes in influential biological pathways in computational models K Alden, J Timmis, PS Andrews, H Veiga-Fernandes, MC Coles IEEE/ACM transactions on computational biology and bioinformatics 14 (2 …, 2016 | 11 | 2016 |
| Application of modeling approaches to explore vaccine adjuvant mode-of-action PR Buckley, K Alden, M Coccia, A Chalon, C Collignon, ST Temmerman, ... Frontiers in Immunology 10, 2150, 2019 | 9 | 2019 |
| Building confidence in quantitative systems pharmacology models: An engineer's guide to exploring the rationale in model design and development J Timmis, K Alden, P Andrews, E Clark, A Nellis, B Naylor, M Coles, ... CPT: pharmacometrics & systems pharmacology 6 (3), 156-167, 2017 | 8 | 2017 |
| Model-driven experimentation: a new approach to understand mechanisms of tertiary lymphoid tissue formation, function, and therapeutic resolution JA Butler, J Cosgrove, K Alden, J Timmis, MC Coles Frontiers in immunology 7, 658, 2017 | 7 | 2017 |
| Utilising a simulation platform to understand the effect of domain model assumptions K Alden, PS Andrews, H Veiga-Fernandes, J Timmis, M Coles Natural computing 14, 99-107, 2015 | 7 | 2015 |
Jon TimmisProfessor of Intelligent and Adaptive Systems, University of SunderlandVerified email at sunderland.ac.uk
