Computational understanding of the immune response to disease
Currently in molecular medicine, we do not have a complete picture of how the most important genes, active during the immune response to fight disease, are processed and transported in cells. Fortunately, the experimental technology has now evolved to allow for “big-data” analyses; such as Next Generation Sequencing (NGS) of all potential genes involved in disease mechanisms. This possibility may equip researchers with an improved understanding of these mechanisms to help discover and improve immunotherapy in the clinic.
In this project the student will work toward developing a bioinformatics application, which taps into this new revolution in molecular medicine; whereby NGS data can potentially be utilized to accelerate discovery of new therapies. The application will be used by clinical bioinformaticians in their computational pipelines to help interpret the results of NGS experiments in the context of processing and transport of key molecules in immune cells. The bioinformatics supervisors will guide the candidate on the most relevant tools and molecular pathway databases to implement the features of the application. The student will gain insights into data mining in clinical bioinformatics and will work closely with one of the leading groups worldwide studying immune recognition molecules, that of Prof. Oddmund Bakke.
The Bakke lab has come far in the characterization of some of the main genes in the processing and transport of foreign “antigens” on specialized structures in immune cells called “MHC complexes”. Data mining of NGS data of immune cells and their antigen processing machinery may propel even further exciting discovery. The Bakke lab, which is a member of a Centre of Excellence, CIR, www.cir.uio.no has at present a patent for a very promising cancer vaccine based on this process, which can “arm” immune cells to kill cancer cells. This may soon be tested in clinical trials and will be an important asset to personalized cancer immunotherapy, which is today on top of the agenda to fight cancer.
It is necessary to have an adequate background in programming and database management, in addition, a desire to apply some statistics and algorithm development.
It is advantageous to have some general understanding of basic cell biology or similar disciplines (physiology, chemistry). However, the candidate will be provided with the supervision and will gain sufficient biological understanding to fulfill the goals of this project.
Background on the Bakke lab: