Course Topics
| Date | Topic | Reading |
| February 2 | Lecture 1: Introduction, review of biochemistry and molecular biology | |
| February 3 | Lecture 2: Computer tutorial, introductory programming | Supplement I |
| February 9 | Lecture 3: Computers and biology, online resources for bioinformatics | Chapter 1, 2 |
| February 10 | Lab 1: Simple pairwise alignment | Chapter 3 |
| February 16 | Lecture 4, Part 1: Pairwise alignment | |
| February 17 | Lecture 4, Part 2: Pairwise alignment | |
| February 23 | Lecture 5: BLAST searching | Chapter 4 |
| February 24 | Lecture 6: BLAST and PHI/PSI-BLAST | Chapter 5 |
| March 2 | Lecture 7: Gene expression and microarrays | Chapter 6 |
| March 3 | Exam I: Biochemistry, programming, and pairwise alignment | |
| March 9 | Lab 3: Microarray data analysis | Chapter 7 |
| March 10 | Lecture 8: Introduction to protein structure and structural databases | Chapter 9 |
| March 16 | Lab 4: Molecular visualization | Supplement II |
| March 17 | No Class | |
| March 23 | No Class - Spring Break | |
| March 24 | No Class - Spring Break | |
| March 30 | Lecture 9: Proteomics | Chapter 8 |
| March 31 | Lab 5: Bioinformatics methods for studying proteins | |
| April 6 | Lecture 10: Multiple sequence alignment | Chapter 10 |
| April 7 | Lab 6: Programming and multiple sequence alignment algorithms | |
| April 13 | Guest Lecture: Protein structure prediction (George Rose) | Supplement III |
| April 14 | Exam II: Microarrays and Proteomics | |
| April 20 | Lecture 11: Phylogeny, cladistics, and evolution | Chapter 11, 12 |
| April 21 | Lab 7: Phylogenetic trees | |
| April 28 | Lecture 12: The human genome project | Chapter 17 |
| April 29 | Lecture 13: Bioinformatics and human disease | Chapter 18 |
| May 4 | Make up day, review for exam | |
| May 5 | Exam III: Phylogenetic analysis, evolution, genomes |
The supplemental reading list is below. Additional readings may be assigned throughout the course.
- Supplement I - “Python Tutorial” by Guido van Rossum. In particular, we will emphasize sections 1-5 and 7. Available at http://docs.python.org/tut/tut.html.
- Supplement II - Gong, H, and Rose G. D. (2005) “Does secondary structure determine tertiary structure in proteins?” Proteins 61 (2): 338-43. [PDF]
- Supplement III - Bradley, P., Misura, K. S. M., and Baker, D. (2005) “Toward High-Resolution de Novo Structure Prediction for Small Proteins.” Science 309 (5742): 1868-1871. [PDF]
Download a complete syllabus here.
