School of Computing, Dublin City University, Ireland

MODELLING & SCIENTIFIC COMPUTING


  
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Research:    Social Systems // Environmental and Transport // Financial and Socioeconomic Modelling // Assisted Living // Biocomputation // Data Science
  

   

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. 

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. Finally, inferential algorithms that aim at building GRN models from these data are developed.  


Selected Group Publications:

  • SÓrbu, A., Ruskin, H. J., and Crane, M., EGIA - Evolutionary Optimisation of Gene Regulatory Networks, an Integrative Approach, Complex Networks V, Studies in Computational Intelligence, Volume 549, 2014, pp. 217-229. DOI: 10.1007/978-3-319-05401-8_21.

  • Marbach, D., Costello, J.C., KŁffner, R., Vega, N., Prill, R.J., Camacho, D.M., Allison, K.R., the DREAM5 Consortium, Kellis, M., Collins, J.J., and Stolovitzky, G. 2012. Wisdom of crowds for robust gene network inference, Nature Methods 9, 796Ė804.

  • SÓrbu, A., Ruskin, H. J., and Crane, M., Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling, Theory In Biosciences, Springer-Verlag, 1-8 , DOI 10.1007/s12064-011-0133-0, 2011.

  • Kerr, G., Perrin, D., Ruskin, H.J., Crane, M. Edge Weighting of Gene Expression Graphs, Advances in Complex Systems, 13:2, 217-238, World Scientific 2010.

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    Image: Microarray and gene expression; source: http://www.microarray.org/sfgf/


    Researchers: Heather J. Ruskin, Martin Crane, John Burns (Assoc.), Ana Barat, Gráinne Kerr (Assoc.), Dimitri Perrin (Assoc.), Alina Sîrbu (Assoc.), Marija Bezbradica, Kabita Shakya; Irina Roznovăţ (Assoc.) Hourieh Hamrah, Andreas Hillmann


       

    Contact: +353 1 700 6747 / modsci@computing.dcu.ie