About me
I joined Jan's group as a Postdoctoral Research Fellow in January 2013, after completing a PhD at the University of York. I was funded by the National Centre for the Replacement, Refinement, and Reduction of Animals in Research (NC3Rs), and a member of the university’s Institute of Microbiology and Infection (IMI). I departed in 2014 to support the development of York Computational Immunology Laboratory.
Research
My principal research interests lie in examining the potential that computer simulation could have in furthering our understanding of biological systems and their impact on human health. This includes looking at frameworks to capture biological information, through to creating, running, and analysing the resultant computer simulation. These simulations could then be used as tools through which initial experiments can be performed prior to any work in the wet-lab, with results of these investigations possibly forming hypotheses for examination in future experimental work. These tools could also have the potential to perform experiments which may be very difficult or impossible to perform in a lab-based environment.
My NC3R funded work at Birmingham aimed to support the recent growth of research into the how the gut microbiota affects human health, in terms of our energy uptake, nutrition, effects on obesity, and use of probiotics. In the short term the aim was to use computer simulation to reduce the number of animal experiments performed in these areas. In the longer term, there is hope that a computational tool could act as a replacement in some studies.
Previously I worked within the Centre of Immunology and Infection (CII) at the University of York, and used similar techniques to explore the development of secondary lymphoid organs in the small intestine. The large majority of this work has been published.
Selected Publications
- K. Alden, M. Read, J. Timmis, P.S. Andrews, H. Veiga-Fernandes, M.C. Coles (2013): spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems. PLoS Computational Biology, Volume 9, Issue 2
- A. Patel, N. Harker, L. Moreira-Santos, M. Ferreira, K. Alden, J. Timmis, K. Foster, A. Garefalaki, P. Pachnis, P.S. Andrews, H. Enomoto, J. Milbrandt, V. Pachnis, M. Coles, D. Kioussis, H. Veiga-Fernandes (2012): Differential RET signaling responses orchestrate lymphoid and nervous enteric system development. Science Signalling, Volume 5, Issue 235
- K. Alden, J.Timmis, P.S. Andrews, H. Veiga-Fernandes, M.Coles (2012): Pairing experimentation and computational modelling to understand the role of tissue inducer cells in the development of lymphoid organs. Frontiers in Immunology. Volume 3. DOI=10.3389/fimmu.2012.00172
- K.Alden (2012): Simulation and Statistical Techniques to Explore Lymphoid Tissue Organogenesis. PhD Thesis
- K. Alden, S. Veretnik, P.E.Bourne (2010): dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics, 11:310
Brief CV
- January 2013 - February 2014: Kreft Group
Research Fellow developing computational tools that can be used to reduce or replace animal experimentation that is currently performed to understand how gut microbiology affects human health. - September 2012 - December 2012: Postdoctoral Research Associate, University of York Developing tool chains for modelling and simulation of the immune system
- September 2009 - September 2012: PhD Student, University of York - Centre for Immunology and Infection and York Computational Immunology Lab
Modelling and simulating the development of gut associated secondary lymphoid organs - September 2008 - September 2009: MRes Computational Biology, University of York and Phil Bourne's Lab at University of California San Diego
Sponsors
My fellowship is funded by NC3R
