Research & Publications

Research Overview

My research focuses on computational modeling of biological systems, particularly plant cell signaling and intercellular communication. I develop mathematical models and simulations to understand complex cellular processes, with a particular interest in transport phenomena and data visualization.

Current Focus Areas

• Computational Biology: Modeling molecular transport in plant cells
• Biophysics Simulations: Narrow escape problems and diffusion processes
• Data Science: High-content analysis using advanced imaging techniques
• Open Source Software: Developing tools for scientific computing

Publications

Journal Articles

2024

• Hughes, A. (2024). “Data Study Group Final Report: Ignota Labs - Toxicity Prediction for Drug Discovery” The Alan Turing Institute. DOI: 10.5281/zenodo.13882192 | Report

2021

• Tomkins, P., Hughes, A., Morris, R.J. (2021). “An Update on Passive Transport in and out of Plant Cells” Plant Physiology. DOI: 10.1093/plphys/kiab406 | PubMed | PMC

• Ohtsu, M. et al. (including Hughes, A.) (2021). “Colletotrichum higginsianum effectors exhibit cell to cell hypermobility” bioRxiv. DOI: 10.1101/2021.01.13.426415

• Hughes, A., Faulkner, C., Morris, R.J., Tomkins, P. (2021). “Intercellular Communication as a Series of Narrow Escape Problems” IEEE Transactions on Molecular, Biological and Multi-Scale Communications. DOI: 10.1109/TMBMC.2021.3083719 | IEEE Xplore

2020

• Hughes, A., Morris, R.J., Tomkins, P. (2020). “PyEscape: A narrow escape problem simulation implementation” Journal of Open Source Software. DOI: 10.21105/joss.02072 | Zenodo

2019

• Hughes, A., Fradgley, N. et al. (2019). “μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives” The Plant Journal. DOI: 10.1111/tpj.14312 | PubMed | PMC

2018

• Cook, F., Hughes, A. et al. (2018). “Barley lys3 mutants are unique amongst shrunken-endosperm mutants in having abnormally large embryos” Journal of Cereal Science. DOI: 10.1016/j.jcs.2018.07.015 | PubMed

2017

• Hughes, A. et al. (2017). “Non-Destructive, High-Content Analysis of Wheat Grain Traits Using X-Ray Micro Computed Tomography” Plant Methods. DOI: 10.1186/s13007-017-0229-8 | PubMed | PMC

Education & Training

Ph.D. in Computational Modelling of Cellular Information Transfer (2018-2022)
John Innes Centre, England, UK

• Conducted forefront research on plant cell signalling in a multidisciplinary team
• Mentored M.Sc. and undergraduate students, enhancing their academic progression
• Published in prestigious academic journals and championed open-source software projects

B.Sc. in Computer Science, First Class Honours (2014-2018)
Aberystwyth University, Wales, UK

• Dissertation led to two notable research publications, highlighting academic prowess

Awards & Recognition

• Software Sustainability Institute Fellowship (2023) - England, UK
• DigiEduHack Climate Change Contest - Finalist (2022) - England, UK
• UK Open Source Awards - Winner (2019) - Wales, UK
• Biotechnology and Biological Sciences Research Council - Fully Funded Ph.D. (2018) - England, UK
• Genetics Society Research Grant - Awardee (2017) - Wales, UK

For more details about any of these projects or potential collaborations, feel free to connect with me via my GitHub or through the blog.