Koide:Home

Click here to see the non-wiki version of this page  Microbial Systems Biology

Our research group is interested in understanding the molecular interactions that define prokaryotes using the Systems Biology approach. We intend to use diverse high-throughput 'omic' technologies, analyze and integrate experimental data using bioinformatics tools and formulate models that describe and predict the behavior of a cell. The integration and exploration of the data and model will raise new hypothesis which will be experimentally tested - validating or refuting the proposed model. This iterative cycle requires the interdisciplinar collaboration between biologists, computer scientist and mathematicians.

To understand and organism as a whole, we are using the archaea Halobacterium salinarum NRC-1 as a model. This unicellular prokaryote thrives in conditions of extreme salinity, it has a compact genome and is easily cultivated and manipulated in the laboratory. It is a fascinating microbe, with potential applications in biotechnology, studies in astrobiology, besides it's role as a model archaea in Systems Biology: six years after the completion of the genome, there is a global gene regulatory network available for Halobacterium salinarum NRC-1.

Our aim is to feed the global gene regulatory model with mechanistic details of gene regulation. We hope that our efforts in inserting molecular mechanisms in a global model will help Synthetic Biology efforts in engineering biological systems.