Staff Profile
Dr Bowen Li
Research Associate
- Email: bowen.li2@ncl.ac.uk
- Address: Level 5,
Urban Sciences Building,
Newcastle upon Tyne
I am currently a Research Associate at Newcastle University in the School of Computing working in Interdisciplinary Computing and Complex BioSystems (ICOS) research group under Dr. Paolo Zuliani.
I received my PhD from Newcastle University in 2017 under the supervision of Prof. Maciej Koutny. My PhD work focused on formal modelling and verification of complex evolving system using Structured Occurrence Nets. After that, I have been working on two EPSRC funded projects (NUFEB and Portabolomics) in Newcastle University. My research focuses on the computational modelling of various biological systems. In the NUFEB project (2016-2019), I worked on the development of individual-based model for modelling and analysis of microbial communities in waster water treatment. In the Portabolomics project (2019-present), I have been working on formal verification of biological models that apply and implement formal methods to model and analyse DNA strand displacement system.
- Xia Y, Jayathilake P, Li B, Zuliani P, Chen J. CFD-DEM modelling of biofilm streamer oscillations and their cohesive failure in fluid flow. Biotechnology and Bioengineering 2021, 118(2), 918-929.
- Gogulancea V, Gonzalez-Cabaleiro R, Li B, Taniguchi D, Jayathilake PG, Chen J, Wilkinson D, Swailes D, McGough S, Zuliani P, Ofiteru ID, Curtis T. Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth. Frontiers in Microbiology 2019, 10, 1871.
- Li B, Taniguchi D, Pahala- Gedara J, Gogulancea V, Gonzalez-Cabaleiro R, Chen J, McGough AS, Ofiteru ID, Curtis TP, Zuliani P. NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities. PLoS Computational Biology 2019, 15(2), e1007125.
- Oyebamiji OK, Wilkinson DJ, Li B, Jayathilake PG, Zuliani P, Curtis TP. Bayesian emulation and calibration of an individual-based model of microbial communities. Journal of Computational Science 2019, 30, 194-208.
- Jayathilake PG, Li B, Zuliani P, Curtis T, Chen J. Modelling bacterial twitching in fluid flows: a CFD-DEM approach. Scientific Reports 2019, 9, 14540.
- Li B, Randell B, Bhattacharyya A, Alharbi T, Koutny M. SONCraft: A Tool for Construction, Simulation and Analysis of Structured Occurrence Nets. In: 18th International Conference on Application of Concurrency to System Design. 2018, Bratislava, Slovakia: IEEE.
- Oyebamiji OK, Wilkinson DJ, Pahala-Gedara J, Rushton SP, Li B, Bridgens B, Zuliani P. A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation. PLOS ONE 2018, 13(4), e0195484.
- Jayathilake PG, Gupta P, Li B, Madsen C, Oyebamiji O, Gonzalez-Cabaleiro R, Rushton S, Bridgens B, Swailes D, Allen B, McGough AS, Zuliani P, Ofiteru ID, Wilkinson DJ, Chen J, Curtis TP. A mechanistic individual-based model of microbial communities. PLoS One 2017, 12(8), e0181965.
- Oyebamiji OK, Wilkinson DJ, Jayathilake PG, Curtis TP, Rushton SP, Li B, Gupta P. Gaussian process emulation of an individual-based model simulation of microbial communities. Journal of Computational Science 2017, 22, 69-84.
- Li B. Visualisation and analysis of complex behaviours using structured occurrence nets. Newcastle University, 2017.
- Li B, Koutny M. Unfolding CSPT-nets. In: PNSE 2015 Petri Nets and Software Engineering. 2015, Brussels, Belgium: CEUR-WS.
- Bhattacharyya A, Li B, Randell B. Time in Structured Occurrence Nets. In: International Workshop on Petri Nets and Software Engineering (PNSE’16). 2016, Torun, Poland: CEUR-WS.org.