Syllabus for BCH-M 628: Introduction to Genomics & Bioinformatics.

Week
1 2 3 4 5 6 Lecture 1 Exercise 1 Lecture 2 Exercise 2 Lecture 3 Exercise 3 Lecture 4 Exercise 4 Lecture 5 Exercise 5 Lecture 6 Exercise 6 Lecture 7 Exercise 7 Lecture 8 Exercise 8 Lecture 9 Final Exam

Topics
Introduction & Biological databases Text based searching of biological databases Introduction to Genome projects Genome viewers Sequence similarity Pairwise alignments & BLAST Multiple sequence alignments; profiles MSA programs and PSI-BLAST Navigating NCBI & EBI Advanced searching of NCBI and EBI Specialized databases & web tools Exploring sequences in depth Predictive methods using protein sequences & gene ontology Protein function prediction & gene ontology Protein-protein interaction networks PPI databases & SMART networks TBA / Hand out final exam Take-home due

Date
5/28/2013 5/30/2013 6/4/2013 6/6/2013 6/11/2013 6/13/2013 6/18/2013 6/20/2013 6/25/2013 7/2/2013

Reading
NCBI paper from NAR Sci. Signaling 5:rs6 (2012) UCSC Genome browser paper (NAR); Ensemble browser paper (BMC Genomics) Chapter 2 and Chapter 4 in Sequence, Evolution, Function by Koonin & Galperin, NCBI Bookshelf Review papers

Website: http://biochem.slu.edu/bchm628 Lectures are in Schwitalla Hall, room 112. Computer lab is in Caroline, 204. Reading material is available for download from the course website. Textbooks you may find useful for background (on reserve at MCL): Introduction to Bioinformatics, 3rd ed., by Arthur M. Lesk A Primer of Genome Science, 4rd ed., by Greg Gibson & Spencer Muse Sequence Evolution Function: Computational Approaches to Comparative Genomics, by E.V. Koonin & M.Y. Galperin; available online as part of NCBI bookshelf.

Last modified: 5/20/2013