Curriculum

The curriculum for programming is the lecture notes on these pages (a PDF version is available by clicking the PDF icon in the top left corner).

Bioinformatics is a rapidly developing field, so textbooks often have parts that need updating. So, in this course, the curriculum for bioinformatics is put together from several sources. We use the best excerpts from the textbooks Understanding Bioinformatics by Jeremy Baum and Marketa J. Zvelebil, Biological Sequence Analysis by Richard Durbin et al., and Exploring Bioinformatics by Caroline St. Clair and Jonathan E. Visick. I have collected the sections from each textbook in separate compendia. You will also be reading short, up-to-date publications on selected topics in bioinformatics.

Below are links to material covering the bioinformatics topics we treat in the course. In the weekly notes, you can see what you need to read to prepare for each lecture. You can also find any curriculum related to the exercises in the weekly note.

Compendia you can download here:

• Compendium of selections from Understanding Bioinformatics
• Compendium of selections from Biological Sequence Analysis
• Compendium of selections from Exploring Bioinformatics

Links to material you need to download yourself (you may need to be on campus or use your student VPN to download from publisher websites):

• Chapter 11: Genome-Wide Association Studies
• Benefits and limitations of genome-wide association studies
• The Theory and Practice of Genome Sequence Assembly
• Alignment methods: strategies, challenges, benchmarking, and comparative overview
• Bioinformatics explained: BLAST (CLCbio)
• Automatic generation of gene finders for Eukaryotic species

Curriculum on webpages (not PDF format):

Using neural nets to recognize handwritten digits (if you have trouble accessing the page, download this zip file with the HTML content, unzip it, and view it locally).