Pathogenomics: Bioinformatics, Transcriptomics and Proteomics  

The genomic era paved the way for new avenues in the applicative research of microorganisms. State-of-the-art technologies for sequencing of complete genomes were developed in recent years, together with an arsenal of tools and high-throughput methodologies for analysis and processing of the data generated. These technologies have revolutionized our approche​s to the study of biological questions and to the strategies for addressing scientific challenges on a genome-wide scale.

Our fields of interest and expertise are:

• Global sequence analyses of pathogen genomes, including: sequence similarity searches; motif, domain, and structure prediction; database mining and functional assignments; database construction, integration and management; cross-genome analyses and comparative genomic studies.
• Analyses of whole genome sequencing (HGS) data; determination of microbial genome sequences and deciphering the composition of unknown samples. 
• Identification of vaccine candidates in whole pathogen genomes: mapping of protein antigens as well as T-cell and B-cell epitopes by immunoinformatic-derived methodologies. 
• Inspection of gene expression profiles by microarray analysis and next-generation RNA-sequencing; pathway and enrichment analyses of complex ‘omics data.
• Analyses of antibody/B-cell high throughput sequencing data and mapping of immune repertoires.

Flowchart presenting down-selection of various subsets of putative MHC binders for experimental evaluation

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Approaches towards profiling the composition of microbial communities

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