- signal transduction
KEY AREA OF EXPERTISE/RESEARCH
computer science, graph theory, computer graphics
If you are interested in any of these aspects and enjoy using cutting edge experimental techniques, we will be delighted to host a fellowship project.
Kojima, K., et al. 2008 Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics 24(12), 1433–41.
Li, W., et al. 2005 A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics 21(9), 2036–42.
Van Iersel, M. P., et al. 2012. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28(15), 2016–21.
Harry Beck's iconic, almost century-old diagram of the London tube guides millions of passengers every day. We are visual creatures and by and large we turn to pictures to gain intuition and understanding. A simplified map of transportation is certainly worth a thousand words. A similar diagram of vast biochemical networks that govern organism’s existence in health and disease is likely to be priceless. If it only existed… For decades researchers have been discovering chemical connections between thousands of bimolecular species in the realm of the living cell. The interactions depend on time and location; hence, the map is not only vastly complex but also changes over time. Unfortunately the increase of our knowledge about biochemical interactions is not on a par with the understanding. This is where the scheme like that of Beck’s will become tremendously helpful.
At SBI we are committed to elucidating molecular mechanism responsible for development of various types of cancer. These mechanisms are nothing else but interactions between biomolecules that appear or vanish during cell’s life. But not all changes in the network’s connectivity lead to development of a disease. Their importance can be evaluated by building mathematical models of the process, however the understanding is greatly enhanced once a visual representation is available. To achieve that, we build a visualization platform that collates known facts about biochemical networks together with experimental data generated in our lab. Such a knowledgebase is further fed into algorithms that draw simplified network schemes and inform us about major routes through which information is passed within the cell in much the same way as Google Maps lets travellers plan their journeys. The ability to browse through various layers of detail is a key not only for understanding the complexity of the system but also for effective communication with other researchers.