Teaching staff
-
Prof. Qi DOU (Instructor)
Dept. of Computer Science & Engineering
Email: qidou@cuhk.edu.hk
Office: Room 1014, 10/F, SHB, CUHK
Consultation hours: Mon 14:00-16:00 -
Prof. Huating WANG (Instructor)
Dept. of Orthopedics & Traumatology
Email: huating.wang@cuhk.edu.hk -
Ms. Yizhen CHEN (TA)
Dept. of Computer Science & Engineering
Email: yzchen@cse.cuhk.edu.hk
Office: Room 1023, 10/F, SHB, CUHK
Consultation hours: Tue 14:00-16:00
Useful links
News
- Welcome to BMEG3102 Spring2021!
- First lecture will start on 13 Jan 2021.
- Piazza homepage is set up!
- Presentation topics are released.
Course information
The goal of this course is to introduce the basic concepts in bioinformatics. Topics to be covered include introduction to bioinformatics, reviews of molecular biology and genetics, biomedical data types and databases, sequence alignment and searching methods, mutation models and molecular phylogenetics, molecular structures, basics of human genetics and genetic diseases, clinical bioinformatics for genetic diseases diagnosis. On the theoretical side, students are expected to learn the relevant knowledge in computer science, biology and mathematics from lectures and tutorials. On the practical side, students are given assignments and tutorials to get hands-on experience in locating, studying and using developed tools to apply the learned concepts in performing standard analytical tasks on biomedical data.
Class time
Lectures:
Wednesdays 10:30 - 11:15
Thursdays 11:30 - 13:15
Tutorials:
Wednesdays 11:30 - 12:15
All lectures and tutorial will use online teaching.
Zoom Room Number: 95602455157
Passcode: 5y845q
Piazza
For discussions and questions:
link: https://piazza.com/cuhk.edu.hk/spring2021/bmeg3102
Assessments:
Assignments:
40%
Class participation:
5%
Reading presentation:
5%
Mid-term examination:
20%
Final examination:
30%
Tentative class schedule
| Week | Time | Topic | Lecturer | Notes | Tutorial | Update | ||
|---|---|---|---|---|---|---|---|---|
| 1 | Jan 13 - 14 | Introduction | Dr. Dou | n/a | 14 Jan | |||
| 2 | Jan 20 - 21 | Sequence alignment and searching (1) | Dr. Dou | 21 Jan | ||||
| 3 | Jan 27 - 28 | Sequence alignment and searching (1) | Dr. Dou | 28 Jan | ||||
| 4 | Feb 03 - 04 | Sequence alignment and searching (2) | Dr. Dou | 04 Feb | ||||
| 5 | Feb 10 | Sequence alignment and searching (2) | Dr. Dou | 10 Feb | ||||
| 6 | Feb 18 | Mutation models and molecular phylogenetics (1) | Dr. Dou | n/a | 18 Feb | |||
| 7 | Feb 24 - 25 | Mutation models and molecular phylogenetics (1) | Dr. Dou | 23 Feb | ||||
| 8 | Mar 03 - 04 | Mutation models and molecular phylogenetics (2) | Dr. Dou | ppt, pdf | 02 Mar | |||
| 9 | Mar 10 - 11 | Motifs and domains | Dr. Dou | 09 Mar | ||||
| 10 | Mar 17 - 18 | Human genetics and genetic disorders | Dr.Wang | pdf1 pdf2 | 16 Mar | |||
| 11 | Mar 24 - 25 | High-throughput data processing and analysis | Dr. Dou | 24 Mar | ||||
| 12 | Mar 31, Apr 01 | Reading week | - - | - - | - - | - - | ||
| 13 | Apr 08 | Functional annotations | Dr. Dou | - - | - - | - - | ||
| 14 | Apr 14 - 15 | Molecular structures | Dr. Dou | - - | - - | - - | ||
| 15 | Apr 21 - 22 | Topic Presentation | Dr. Dou | - - | - - | - - | ||
Presentation topics
1. Protein folding prediction with AI
DeepMind’s protein-folding AI has solved a 50-year-old grand challenge of biology
2. COVID and bioinformatics
AIs that read sentences are now catching coronavirus mutations
3. Functional genomics data privacy
‘Sanitizing’ functional genomics data may prevent privacy breaches
4. Gut Microbiota and Human Health
We are what we eat
5. Cancer diagnosis
Cancer mutations occur decades before diagnosis
6. Discover the genetic patterns of complex diseases
Bioinformatic study underscores contribution of tandem repeat mutations in Autism
7. The next wave after single-cell analysis: spatial single-cell transcriptomics
Method of the Year, spatially resolved transcriptomics
8. Genome-Based drug repurposing
Systematically prioritizing candidates in genome-based drug repurposing
9. Beyond the base sequences
Genomics analysis moves to the next level
10. Methods to assess off-target CRISPR edits
Three of a Kind: New study grades methods to assess off-target CRISPR edits
Reference materials
- Bioinformatics Micro-modules, YouTube channel, by Prof. Kevin Yip.
- Fundamental Concepts of Bioinformatics, by Dan E. Krane, Michael L. Raymer and Benjamin Cummings, Pearson Education, 2003.
- Algorithms in Bioinformatics: A Practical Introduction, by Wing-Kin Sung, Chapman & Hall, 2009.
[with free online materials]