Fall Semester

Crash course on Computational Biology for Computer Scientists

Lecturer: Bartek Wilczyński (University of Warsaw).

About the lecturer | Course Summary | Slides: 1 2 3 | Assignment

About the lecturer: Bartek Wilczyński obtained his Msc in Computer Science at MIM UW, then he received a phd in Mathematics at Institute of Mathematics of Polish Academy of Sciences in Warsaw. After that he did a post doctoral fellowship at the European Molecular Biology Laboratory in Heidelberg in Germany. Since 2011, he is working here in Warsaw on the problems in broadly defined computational biology. His main research interests are focused on questions related to how computational models can help us understand the mechanisms of multicellular system development.

Course summary: The course will cover the topics from computational biology that are in different ways relevant for graduate students in computer science. The lecture will be organized around biology-motivated problems and will discuss wide range of computational tools to address them. We will discuss the very basic notions of biological sequence comparisons: how they lead to computationally difficult problems and what heuristic approaches are used to solve them. We will cover phylogenetic trees and their properties that might lead to interesting computational problems. We will talk about very current and practical problems in the next generation DNA sequencing area and how their solutions utilize de Bruijn graphs and Ferragina-Manzini indexes. Finally, we will also cover some structural problems including protein and chromosome structure prediction.

Assignment: You can find the problem set here. Please send the solutions to the address provided on the problem sheet by Wednesday, December 21.