BioComputation Research Lab at DCU

Biocomputation or scientific computing for the biosciences is the application of sophisticated computational algorithms and high performance/distributed computer systems to wide-ranging problems in the biotechnology field. Examples include microarray data analysis, drug transport (pharmacokinetics; in vitro and in vivo) and virus propagation modelling, both of which impact directly on the work of the NICB and offer exciting inter-disciplinary challenges. 

Modelling immune response to viral invasion

The aim of this project on modelling immune response to viral invasion, specifically Human Acquired Immuno-Deficiency Syndrome (associated with HIV infection), is to explore the population dynamics for different cell types, based on what is understood or conjectured about cellular mechanisms. The initial focus will be to describe macroscopic .latency. on a microscopic basis, quantifying the stages of helper T-cell decline, in order to identify crucial crossover points and thresholds for viral population explosion. Second, this project will seek to improve biological reality by incorporating features from models which attempt detailed descriptions of all cell types involved in the viral invasion/ immune response reaction (e.g. the Seiden and Celada model for HIV; ARIC library). Intra- and inter-cellular interactions will be investigated in detail, to explore cell survival characteristics and to quantify the influence of additional cell types on disease progression. The viability of adapting some of these ideas to modelling features of other immuno-suppressive disorders will be explored. 

Drug dissolution / predicition - pharmacokinetics

A computational pharmacokinetics approach will be used to develop a package for cheap, reliable and fast prediction of drug absorption by the body from a localised source. The precise control of drug input to the body by different routes is now possible using a variety of sophisticated delivery systems. However, most drugs are still given as conventional oral dosage forms or simple injections, methods of drug delivery that can be variable and unpredictable. Of particular interest in the design of effective drug delivery systems is the rate of drug release into the human body from the tablet or implant used to deliver the dosage. A more effective drug delivery system would release the drug more gradually over time, using materials which maintain a constant surface area of the drug. This project will investigate the role of computational pharmacokinetics for the development of more accurate drug dissolution models in vitro and in vivo and the use of these models in the simulation of drug transport. This research will involve interaction with NICB research on anticancer drug assays and the Bioassays and Bioanalysis Core Facility. 

Microarray Data Analysis

The availability of time series mRNA expression data sets has spurred the race to infer Genetic Regulatory Networks (GRNs) to explain trend and causal relationships among genes measured in microarray experiments.  As a complement to such techniques Dimension Reduction Techniques, borrowing from experience on financial time series can be used to add further insight to such complex datasets.  Finally,
Novel Database Models will be developed to make use of the natural inter-relationships between data arising from microarray experiments carried out according to, for example, the MIAME standard.
 

Recent Topics as Part of the MSc in Bioinformatics Practicum Series:

• Agent Based Modelling of Bacteria and Antibiotics
• Tissue MicroArrays
• Virtual Slides in Pathology
• Analysis of Microarray Data
• Use and refinement of software tools for protein sequence and structural comparisons
• Motif identification through multiple sequence alignment
• Navigating Biomedical Publication Databases
• Protein and Gene Sequence Matching Algorithms
• Large-scale distributed multiprocessor simulation of genealogy
• Frequency domain models for HIV infection
• Differential Equation models for HIV infection

Researchers: Heather J. Ruskin, Martin Crane, John Burns, Ana Barat, Niall McMahon, James Murphy, Gráinne Kerr, Ashley Callaghan, Ed McGuinness, Dimitri Perrin