CS466: Introduction to Bioinformatics
Lecture Zoom, 12:30PM - 1:45PM, T/R
Instructor: Jian Peng
Associate Professor of Computer Science
Email: jianpeng@illinois.edu
Office Hour Zoom: Same as
lecture
Office Hour: 3:00pm - 4:00pm Monday
Teaching Assistant: Baqiao Liu
PhD Student of Computer Science
Email: baqiaol2@illinois.edu
Office Hour Zoom: Link
Office Hour: 1:30pm - 2:30pm Friday
Teaching Assistant: Shayan Tabe Bordbar
PhD Student of Computer Science
Email: tabebor2@illinois.edu
Office Hour Zoom: Link
Office Hour: 4:00pm - 5:00pm Monday
Lecture Zoom: Meeting ID
Time: 12:30PM - 1:45PM, T/R
Forum: piazza
Course Objectives
Introduction to bioinformatics:
- Basic problems in computational biology
- Statistics and machine learning for data analysis
- Algorithms for data processing
- Advanced applications to biology
Prerequisites
- Programming skills (equivalent to CS 225) for doing the mini-project.
- Knowledge of basic probability and statistics for understanding several lectures.
- No biology background is necessary.
Reading Assignments
Problem sets for the final exam. As written on Piazza, the final exam questions will be a subset of these problems. Please note that we will not provide any guidance/solution for these problems and we hope that you can work on all the problems and make sure you understand how to solve them.
Molecular
Biology for Computer Scientists by Larry Hunter.
Grading Scheme
- Five problem sets (30%)
- Midterm (30%)
- Final (40%)
Assignments Policy
- Please see the University Policy on Academic Integrity, especially the section on plagiarism.
- Late submission within 3 days (72 hours) is worth 80% credit.
- A student may request an extension of 3 days without costing credits at most once in the semester.
Schedule
| Date | Recording | Slides |
|---|---|---|
| 01/26/2021 | Media Space | Introduction [slides] |
| 01/28/2021 | Media Space | Molecular Biology [slides] |
| 02/02/2021 | Media Space | Probability & Statistics [slides] |
| 02/04/2021 | Media Space | Probability & Statistics, Sequences [slides] |
| 02/09/2021 | Media Space | Biological Sequences [slides] |
| 02/11/2021 | Media Space | Sequence Alignment [slides] |
| 02/16/2021 | Media Space | Sequence Alignment [slides] |
| 02/18/2021 | Media Space | Alignment Review [slides] |
| 02/23/2021 | Media Space | Pattern [slides] |
| 02/25/2021 | Media Space | Pattern II [slides] |
| 03/02/2021 | Media Space | Pattern III [slides] |
| 03/04/2021 | Media Space | Pattern IV [slides] |
| 03/09/2021 | Media Space | BLAST [slides] |
| 03/11/2021 | Media Space | BLAST [slides] |
| 03/16/2021 | Media Space | BLAST [slides] |
| 03/18/2021 | Zoom | — |
| 03/23/2021 | Zoom | Midterm Review [slides] |
| 03/30/2021 | Zoom | BLAST [slides] |
| 04/01/2021 | Zoom | Sequence Assembly [slides] |
| 04/06/2021 | Zoom | Assembly, HMM [slides] |
| 04/08/2021 | Zoom | HMM [slides] |
| 04/15/2021 | Zoom | HMM, Gene Finding [slides] |
| 04/20/2021 | Zoom | HMM [slides] |
| 04/22/2021 | Zoom | Classification [slides] |
| 04/27/2021 | Zoom | Machine Learning [slides] |
| 04/29/2021 | Zoom | Machine Learning [slides] |
| 05/04/2021 | Zoom | Final Review [slides] |
Assignments
Please submit on Gradescope (with entry code V8WNZV in case you are not enrolled in the class yet.)
| Release Date | Due Date | Assignment | Solution |
|---|---|---|---|
| 02/21/2021 | 03/03/2021 (Wed.) 11PM | [PDF] [Docx] | See Piazza. |
| 03/17/2021 | 03/23/2021 (Tue.) 11:59PM | [PDF] [Docx] | See Piazza. |
| 04/08/2021 | 04/15/2021 (Thur.) 11:59PM | [PDF] [Docx] | — |
| 04/29/2021 | 05/15/2021 (Sat.) 11:59PM | [PDF] | — |
| 04/14/2021 | 05/15/2021 (Sat.) 11:59PM | [PDF] | — |