Thursday, July 14, 2011 - 3.00 pm
Building E - Room 1

Dr. Alina Sirbu
Centre for Scientific Computing and Complex Systems Modelling
School of Computing, Dublin City University, Ireland

Gene regulatory network modelling with evolutionary algorithms - an integrative approach

ABSTRACT
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Building models for gene regulation has been an important aim of
Systems Biology over the past years, driven by the large amount of
gene expression data that has become available with the development of
high throughput measurement techniques. In this presentation, an
integrative parallel framework for GRN modelling is introduced, which
employs evolutionary computation and different types of data to
enhance model inference. Integration is performed at different levels.
(i) An analysis of cross-platform integration of time series
microarray data, discussing the effects on the resulting models and
exploring cross-platform normalisation techniques, is presented. (ii)
Other types of measurements and knowledge, such as knock-out
experiments, annotated transcription factors, binding site affinities
and promoter sequences are integrated within the evolutionary
framework to obtain more plausible GRN models. Furthermore, (iii),
RNA-seq data is studied in comparison to microarray experiments, to
identify overlapping features and possibilities of integration within
the framework.