Meta analysis algorithms for microarray gene expression data using Gene Regulatory Networks
Using microarrays, researchers are able to obtain a genome wide snapshot of a biological system under a given experimental context. Fortunately, a significant amount of gene regulation data is publicly available through various databases. We present a ...
Learning Bayesian networks with integration of indirect prior knowledge
A Bayesian network model can be used to study the structures of gene regulatory networks. It has the ability to integrate information from both prior knowledge and experimental data. In this study, we propose an approach to efficiently integrate global ...
Using Gene Ontology to enhance effectiveness of similarity measures for microarray data
Reducing redundancy is an important goal for most feature selection methods. Almost all methods for redundancy reduction are based on the correlation between gene expression levels. In this paper, we utilise the knowledge in Gene Ontology to provide a ...
Assessment of length distributions between non-coding and coding sequences amongst two model organisms
The availability of genomic DNA and cDNA sequence data has escalated the data mining and genomics era. We aim to investigate the length distributions of the non-coding and coding regions of protein genes of two model organisms, Arabidopsis thaliana and ...
Invariance kernel of Biological Regulatory Networks
The analysis of Biological Regulatory Network (BRN) leads to the computing of the set of the possible behaviours of the biological components. These behaviours are seen as trajectories and we are specifically interested in cyclic trajectories since they ...
bcnQL: A query language for biochemical networks
This paper proposes a graph data model that can represent information present in Biochemical Networks. The study presented in this paper also proposes a query language, called bcnQL, which empowers users to query entities, interactions, processes and ...
Genome-wide DNA-binding specificity of PIL5, an Arabidopsis basic Helix-Loop-Helix (bHLH) transcription factor
PIL5 is a member of the basic Helix-Loop-Helix (bHLH) transcription factor superfamily. We previously showed that PIL5 binds to the G-box (CACGTG) motif with high affinity. However, since there are many randomly matched G-box motifs throughout the ...
A hybrid clustering algorithm for identifying modules in Protein Protein Interaction networks
Identifying modules in Protein Protein Interaction (PPI) networks is important to understand the organisation of the cellular processes. In this paper, we present a novel algorithm combining Molecular Complex Detection (MCODE) with Girvan Newman (GN) to ...