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Research interests

Np-complete problems in biology; transcription regulation, comparative regulomics, pattern recognition and large-scale genome sequencing methods.

All our research is performed in silico. Projects that require 'wet-lab' experimentation and verification, we rely on our collaborators.

Home > Research > Current projects

Current research projects

1. Analysis of non-allergenic, allergen like proteins and cross-reactivity. Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult.

2. Analysis and prediction of gene regulatory pathways. Every level of organization has its unique properties that are more than just a sum of the components. Genes are regulated in many complex ways responding to internal and external signals, depending on the environment and the previous history of the specific differentiation of a cell, thus yielding unique properties at each specific level.

3. Prediction of RNA 3D structure.

4. Specific functions of histone demethylases and their evolutionary relationships.

5. Sequencing / analysis of virulence of highly resistant bacterial strains.

6. Analysis tools for second generation sequencing methods.

7. Sequencing, analysis, annotation and knowledge base for the Black Tiger Shrimp. Several large genomes have been completely sequenced, but despite of shrimp’s economic and scientific importance no large-scale sequencing project has been initiated yet. The availability of a shrimp genome will provide a basis for increased understanding of the fundamental biology of shrimp and immediate applications for selective breeding and increase the knowledge of genomes themselves. In comparison to agriculture species, such as pig, cow and chicken whose genome has been completely sequenced, relatively little has been done for aquaculture species. The knowledge of these species is also fragmented, in particular of shrimp, despite of its high production value in aquaculture.

8. Known and novel viruses in our envinroment. Potential future outbreaks, novel genes and evolution of virulence.