Mehmet Serkan Apaydın

Advanced bioinformatics is a practical, hands-on approach recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of genomes, sequences and proteins. Various existing methods will be critically described and the strengths and limitations of each will be discussed. There will be practical assignments utilizing the tools described. All homework and coursework must be submitted electronically. The course will follow closely a class on Computational Molecular Biology taught by Prof. Doug Brutlag at Stanford University (http://biochem218.stanford.edu). We will cover additional topics as well. You are encouraged to bring a laptop to the class and repeat the demos made by the instructor.

There will be homework assignments utilizing the tools described in the lectures. All homework and final projects will be submitted in electronic form, as e-mail or e-mail attachments. A final paper will be required for the course that critically and constructively analyzes one of the areas presented in the course. The final project may also present a novel application of existing tools or the development of some new or improved method. There will be a short presentation (10 mins) of the project in one of the last two lectures and a write-up. The homework will count for 35% of the final grade and the project will count for 65%.

Here is a tentative schedule: