In a certain sense, many fundamental biological processes can be viewed as performing computation and communication (e.g., gene transcription and regulation). From this point of view, it is interesting to ask what application computational methods have in deciphering and understanding biological processes. We will look at how computational approaches have played an active role in helping us understand biological processes, and how these approaches may even inform our understanding of the processes themselves. (more)
No previous knowledge of biology or biochemistry will be assumed; we will spend the first few weeks of class covering the prerequisite material. After covering prerequisite material, the lecture schedule will consist of presentations by me, student presentations, and guest lecturers. Your course grade will be determined (equally) by student presentations and a semester project. (more)
Date |
Reading |
Presenter |
Class Topic |
| Feb 1 | — | Ram | Administrivia and Overview (PDF) (Powerpoint) |
| Feb 6 | NCBI Genetics Primers | Ram | Intro to Genetics & Molecular Biology (PDF) (Powerpoint) |
| Feb 8 | — | Ram | Intro to Computation (Powerpoint) (PDF) |
| Feb 13 | 1, 2, 3, 4 | Ram | Dynamic Programming and Sequence Alignment Algorithms (Powerpoint) (PDF) |
| Feb 15 | 1, 2, 3, 4, Assembly Tutorial | Ram | Algorithms for Sequence Assembly (Powerpoint) (PDF) |
| Feb 20 | — | — | President's Day |
| Feb 22 | Cartoon Guide pages 164--178, Overview of Transcription, 1, 2, 3 | Ram | Transcription and Gene Regulation (Powerpoint) (PDF) |
| Feb 27 | 1, 2 | David Kulp (CS) | Gene Finding/Microarray Analysis (PDF) |
| March 1 | 1, 2, 3, 4 | Manju | Genetical Genomics (Powerpoint) (PDF) |
| March 6 | — | Manju | Genetical Genomics (Powerpoint) (PDF) |
| March 8 | 1 | Ram | Introduction to Protein Structure (Powerpoint) (PDF) |
| March 13 | 1, 2, 3, 4 | Naomi | Theory and Practice of Molecular Dynamics (Powerpoint) (PDF) |
| March 15 | — | Naomi | Theory and Practice of Molecular Dynamics |
| March 20 | — | — | Spring Break |
| March 22 | — | — | Spring Break |
| March 27 | 1, 2, 3, 4 | Jon | Protein Structure Prediction (Powerpoint) (PDF) |
| March 29 | — | Jon | Protein Structure Prediction |
| March 31** | 1, 2 | Oliver Brock (CS) | Protein Structure Prediction (Powerpoint) (PDF) |
| April 3 | 1, 2, 3, 4 | Witold | Protein Redesign for Allostery (Powerpoint) (PDF) ) |
| April 5 | — | Witold | Protein Redesign for Allostery |
| April 10 | — | — | Class Cancelled |
| April 12 | 1, 2, 3, 4 | Shiva | Computation of Protein Geometry (PDF) |
| April 14** | — | Shiva | Computation of Protein Geometry |
| April 17 | — | — | Patriot's Day |
| April 19 | 1, 2, 3, 4, 5 | Kristen | Homology Modeling via Protein Threading (Powerpoint) (PDF) |
| April 21** | — | Kristen | Homology Modeling via Protein Threading |
| April 24 | — | Jeanne Hardy (Chemistry) | X-Ray Crystallography (PDF) |
| April 26 | 1, 2, 3, 4 | Nivya | NMR Data and Protein-Protein Docking (Powerpoint) (PDF) |
| April 28** | — | Nivya | NMR Data and Protein-Protein Docking |
| May 1 | 1, 2, 3, 4 | Bhargavi | Evolutionary Analysis of Protein Structure |
| May 3 | — | Bhargavi | Evolutionary Analysis of Protein Structure |
| May 8 | 1, 2, 3, 4 | Sameer | Graph-based Approaches to Interpreting Biological Networks |
| May 10 | — | Sameer | Graph-based Approaches to Interpreting Biological Networks |
| May 15 | 1, 2*, 3, 4, 5 | Rafael | Applications of Control Theory to Analyzing Biological Networks |
| May 17 | — | Rafael | Applications of Control Theory to Analyzing Biological Networks |
* - Optional Reading ** - Substitute or additional lecture.