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A systems understanding of Parkinson's disease
This project takes a systems approach to disease by considering it in the same way that a control systems engineer might analyse faults in a complex technological process. See the study document A Systems Approach to Parkinson's Disease for more general description of the approach. For research topics within this area see the project descriptions of Stuart Butler, Mathieu Cloutier and Míriam García.
Contact:
Peter Wellstead
Collaborator(s):
University of Rostock
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Modelling and analysis of signal transduction networks
Signal transduction networks are responsible for many important changes
of cellular behaviour. We are involved in modelling apoptotic and alternative cell death signalling pathways by comprehensive systems modelling. The aim is to identify the molecular control mechanisms regulating cell death and survival in mammalian cells. In addition, we develop system analysis methods specifically suited for this class of models and perform model analyses such as identifiably and sensitivity analysis. For more details please visit the IMMT web pages.
Contact:
Eric Bullinger (Visiting Senior Lecturer) and Dimitris Kalamatianos
Collaborator(s):
RCSI, University of Stuttgart and University of Strathclyde.
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A systems understanding of the signalling pathways associated with neurological disorders
This is a collaborative project with the University of Limerick and the Department of Computer Science, NUI Maynooth. Using in vivo microdialysis data generated by Dr William O' Connor and his team we are building bio-informatic tools for understanding and interpreting signalling pathway model data.
Contact:
Stuart Butler and
Peter Wellstead
Collaborator(s):
University of Limerick and
Department of Computer Science, NUIM
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Understanding the brain energy metabolism
The objective of this project is to use mathematical models that will help us understand how deterioration of the brain energy metabolism might lead to failures on cellular sub-systems. Our first stage is the modelling of the energy metabolism, using prior work by Aubert and coworkers, and cross validation with in-vivo data from the Lowry laboratory.
Contact:
Mathieu Cloutier
Collaborator(s):
John Lowry (Department of Chemistry, NUIM)
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The role of oscillatory theory in brain function
The recent developments in Deep Brain Stimulation (DBS) as a treatment for Parkinson's Disease, plus remarkable results with electro stimulation of comatose patients, lead us to inquire how these treatments work. We start with the proposition that DBS may perform some desynchronisation function and electro stimulation performs some resynchronisation. From this we investigate the theoretical and computational properties of these in large groups of coupled oscillatory connections in a way that simulates the axonal connections between different brain regions.
Contact:
Míriam García
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Live cell image analysis
This project is part of the ITC2 research project of the National Biophotonics and Imaging Platform (NBIP) funded by the Irish Government and focuses on the development of a novel automated monitoring system for live cell imaging based on real time evaluation. Our scope is to develop a robust real-time image analysis and modelling solution along with its associated development environment. Both the algorithms and associated software will be made available to all NBIP partners via a software workbench. For more details please visit the IMMT web pages.
Contact:
Dimitris Kalamatianos and Eric Bullinger (Visiting Senior Lecturer).
Collaborator(s):
RCSI, UCC and University of Strachclyde.
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Analysis of Biological Interaction Networks
Recent developments in experimental methodologies have generated an unprecedented volume of data on the structural properties of biological networks. This has in turn led to a need for novel computational techniques and mathematical frameworks tailored to the analysis of the networks whose structure is still emerging. We are primarily interested in developing and analysing algorithms to infer gene and protein function from the structure of interaction networks, and in the impact of false and incomplete data on such algorithms. A related strand of research is concerned with the design of efficient sampling strategies for identifying the structure of complex networks in biological systems.
Contact:
Oliver Mason
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Optimality principles in metabolic regulation
This project aims to study optimality principles that can explain the dynamics of metabolic networks. This idea is based on the premise that evolutionary processes have optimized the design of these networks such that certain properties relevant to cellular fitness are preserved. Using optimization concepts from Systems and Control Theory, we aim to establish design principles that provide insight into kinetic and structural properties of metabolic networks. Furthermore, this approach may stimulate the development of new control-theoretic concepts especially taylored for metabolic systems.
Contact:
Diego Oyarzún
Collaborator(s):
Brian Ingalls (University of Waterloo)
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Live Cell Image Analysis
This project is part of the ITC2 research project of the NBIP and focuses on the development of a novel automated monitoring system for live cell imaging based on real time evaluation. Our scope is to develop a robust real-time image analysis and modelling solution along with its associated development environment. Both the algorithms and associated software will be made available to all NBIP partners via a software workbench. The ITC2 project partners research programmes in the following cores of the NBIP: Molecular and Cellular Imaging Core (RCSI), Compute Node (UCC) and elements within the Imaging Technology Core (RCSI, NUIM).
Contact:
Perrine Paul
Collaborator(s):
Heinrich Huber (RCSI/SIEMENS Ireland)
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Synchronization of Biological Oscillations
The objective of this project is to contribute to a mathematical theory of synchronization, with applications in biology. Building on recent theoretical results on global phase-locking in populations of phase-coupled oscillators, our aim is to provide a mathematical characterization of the biological mechanisms of synchronization. The work will be based in part on several case studies, including: (1) glycolytic oscillations in yeast; (2) calcium oscillations in non-excitable cells; (3) circadian oscillations in the suprachiasmatic nucleus (SCN).
Contact:
Mark Verwoerd
Collaborator(s):
Frank Doyle III (UCSB)
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