Research

In the Bioinformatics Department we are working on computational methods that act as bridges between molecular biology, systems biology and molecular medicine, exploiting computational intelligence, high performance computing and network analysis

In the Bioinformatics Department we are working on computational methods that act as bridges between molecular biology, systems biology and molecular medicine, exploiting computational intelligence, high performance computing and network analysis. More specifically, we are working on the following directions:

Build pipelines to analyze omics from various sources regarding the profiling of the transcriptome (RNA-seq), the genome (DNA-seq, exome-seq), and the proteome (MS data).

Create post-filtering methodologies to derive meaningful molecular signatures of the diseases.

Develop computational methodologies for classification and clustering on molecular data in order to rank them based on their significance to the disease towards biomarker discovery, risk estimation and early prediction.  

Proceed to omics-driven Network Reconstruction using Network Inference methods as well as Probabilistic methods (Random Walks on Nets).

Perform Biological Network Analysis in terms of Quantitative Measures of Network Complexity.

Perform re-ranking for the derived gene/protein lists (in a biomarker discovery pipeline) based on their systemic/network characteristics.

Perform drug repurposing pipelines based on the expression profiles for each patient.

Proceed with Chem-Bioinformatics concerning compound screening, fingerprint calculation and analysis, toxicity checks, to conclude with short listed compounds suitable to the profile of each patient.

Develop and utilize methods of image analysis and computational intelligence to process, analyze and understand biomedical signals and images in order to extract critical features acting as imaging markers for various diseases or stages of a disease.

Develop systems for computer aided diagnosis that integrate molecular, imaging and clinical data towards risk estimation adapted to each patient profile.

Create handy and powerful Databases that will give dynamic feedback to new-comers case analyses through content-based retrieval approaches.

Create user-friendly Bioinformatics Web Services to have medical doctors actually use the developed tools.

Selected Recent Publications:

M. Zachariou, G. Minadakis, A. Oulas, S. Afxenti, G. M. Spyrou. “'Integrating multi-source information on a single network to detect disease-related clusters of molecular mechanisms”, Journal of Proteomics, In Press

Oulas A, Minadakis G, Zachariou M, Sokratous K, Bourdakou MM, Spyrou GM. Systems Bioinformatics: increasing precision of computational diagnostics and
therapeutics through network-based approaches. Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx151. 

Bourdakou MM, Spyrou GM. Informed walks: whispering hints to gene hunters inside networks' jungle. BMC Syst Biol. 2017 Oct 11;11(1):97. doi:
10.1186/s12918-017-0473-6. 
 

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