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

  • Ms. Qinyao LI (TA)

    Dept. of Computer Science & Engineering
    Email: qyli21@cse.cuhk.edu.hk
    Office: Room 1013, 10/F, SHB, CUHK
    Consultation hours: Mon 15:00-17:00

Useful links


  • Welcome to BMEG3102 Spring2022!
  • First lecture will start on 11 Jan 2023.
  • Piazza homepage is set up!

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, 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 and venue


Wednesdays      10:30AM - 11:15AM (SC L5)
Thursdays          11:30AM - 01:15PM (SC LG23)


Wednesdays      11:30AM - 12:15PM (SC L5)


For discussions, questions and sharings:
link: https://piazza.com/cuhk.edu.hk/spring2023/bmeg3102


Assignments:                              45%
Topic presentation & report:        15%
Final examination:                       35%
Class participation:                       5%

Tentative class schedule

Week Time Topic Assignment

1 Jan 11 - 12 Introduction --
2 Jan 18 - 19 Sequence alignment and searching (I) --
3 Jan 25 - 26 Lunar new year holiday --
4 Feb 01 - 02 Sequence alignment and searching (I) Asg 1
5 Feb 08 - 09 Sequence alignment and searching (II) --
6 Feb 15 - 16 Sequence alignment and searching (II) --
7 Feb 22 - 23 Mutation models and molecular phylogenetics (I) --
8 Mar 01 - 02 Mutation models and molecular phylogenetics (II) Asg2
9 Mar 08 - 09 Reading week --
10 Mar 15 - 16 Motifs and domains --
11 Mar 22 - 23 High-throughput data processing and analysis (I) --
12 Mar 29 - 30 High-throughput data processing and analysis (II) Asg 3
13 Apr 6 Functional annotations --
14 Apr 12 - 13 Molecular structures Asg 4
15 Apr 19 - 20 Topic presentation --

Presentation topics

1. Protein folding prediction with AI
Highly accurate protein structure prediction with AlphaFold
2. COVID and bioinformatics
AIs that read sentences are now catching coronavirus mutations
3. Functional genomics data privacy
Functional genomics data: privacy risk assessment and technological mitigation
4. Protein function prediction
Structure-based protein function prediction using graph convolutional networks
5. Cancer diagnosis
The evolutionary history of 2,658 cancers
6. Discover the genetic patterns of complex diseases
Repeat DNA expands our understanding of autism spectrum disorder
7. The next wave after single-cell analysis: spatial single-cell transcriptomics
Method of the Year, spatially resolved transcriptomics
8. Genome-Based drug repurposing
Opportunities for drug repositioning from phenome-wide association studies
9. Transcription factor binding sites prediction
Deep neural networks identify sequence context features predictive of transcription factor binding
10. Methods to assess off-target CRISPR edits
Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9
11. Sequence assembly
Chromosome-scale, haplotype-resolved assembly of human genomes
12. Multimodal Single-Cell Data Integration
Computational principles and challenges in single-cell data integration

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]

© BMEG3102 | Spring2023 | The Chinese University of Hong Kong