Syllabus for BCH-M 628: Introduction to Genomics & Bioinformatics. Week
Topics
1
Lecture 1
Introduction & Biological databases
Exercise 1
Text based searching of biological databases
2
Lecture 2
Introduction to Genome projects
Exercise 2
Genome viewers
Lecture 3
Sequence similarity
Exercise 3
Pairwise alignments & BLAST
3
Lecture 4
Multiple sequence alignments; profiles
Exercise 4
MSA programs and PSI-‐BLAST
Lecture 5
Navigating NCBI & EBI
Exercise 5
Advanced searching of NCBI and EBI
4
Lecture 6
Specialized databases & web tools
Exercise 6
Exploring sequences in depth
Lecture 7
Exercise 7
5
Lecture 8
Protein-‐protein interaction networks
Exercise 8
PPI databases & SMART networks
Lecture 9
6
Final Exam
Predictive methods using protein sequences & gene ontology Protein function prediction & gene ontology
Date
Reading
5/28/2013
NCBI paper from NAR
Sci. Signaling 5:rs6 (2012)
5/30/2013
UCSC Genome browser paper (NAR); Ensemble browser paper (BMC Genomics)
6/4/2013
Chapter 2 and Chapter 4 in Sequence, Evolution, Function … by Koonin & Galperin, NCBI Bookshelf
6/6/2013
6/11/2013
6/13/2013
6/18/2013
6/20/2013
TBA / Hand out final exam
6/25/2013
Review papers
Take-‐home due
7/2/2013
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