00.0 Introduction to the course "Epigenetics 2025" [Loi] - 01/3/2025
00.1 Epigenetics, Epigenomics and Its Applications [Loi] - 01/3/2025
01.0 Principles of Epigenetics [Loi] - 08/3/2025
01.1 Basic Bash Script and Awk [Thanh] - 08/3/2025
Practice: 
02.0 Chromatin based epigenetic control I [Loi] - 15/3/2025
02.1 Basic programing with R [Huy] - 15/3/2025
- PPTX
- Practice:
03.0 Chromatin based epigenetic control II [Loi] - 22/3/2025
03.1 Statistical analysis with R [Huy] - 22/3/2025
- PPTX
- Practice:
- Exercise 1. Explain Figure 1 in the paper
- Exercise 2. Explain Figure 7A in the paper
- Exercise 3. Explain Figure 5E in the paper
- Exercise 4. Explain Figure 4C and 4D in the paper
- Exercise 5. Explain Figure 1F and 1H in the paper
04.1 Hands-on: Deeptools and CSAW [Tam] - 29/3/2025
- PPTX: Deeptools and CSAW
- Practice: deeptools
, csaw
- Dataset for homework Here is BAM files and gene regions for chr19. Please download these datasets and replicate the codes provided in the lecture (Datasets used for lecture are of chr22).
05.0 DNA-methylation and epigenetic control [Loi] - 05/4/2025
- Exercise 1. Explain Figure 5 in the paper
- Exercise 2. Explain Figure 3 in the paper
- Exercise 3. Explain Figure 4 in the paper
- Exercise 4. Explain Figure 5 in the paper
- Exercise 5. Explain Figure 2 & 3 in the paper
05.1 Data visualization with R [Tuan Thanh] - 05/4/2025
- PPTX
- Practice:
06.0 DNA methylation analysis with DMRcate [Thien/Hoang] - 12/4/2025
- Introduction to DMR
- Data - LINK1
- Data.gz - LINK2
- 00.Install_packages:
- 01.GSE2IDAT_&_IDAT2Table:
- 02.DMRcate:
- 03.Plotting:
- 04.Annotation:
- 05.Gene ontology analysis:
06.1 DNA methylation visualization with IGV [Kim] - 12/4/2025
- Practice:
07.0 Non-coding long and small RNAs in epigenetic control [Loi] - 19/4/2025
microRNA
Class Exercises
- Exercise 1. Explain Figure 1 to 8 in the paper
- Exercise 2. Explain Figure 4 in the paper
- Exercise 3. Explain Figure 3 in the paper
- Exercise 4. Explain Figure 4 in the paper
- Exercise 5. Explain Figure 2, 4 and 5 in the paper
07.1 ENCODE database and Visualizing epigenomics with UCSC Genome Browser [Tuan Thanh] - 19/4/2025
08.0 Mechanisms of epigenetic control during development [Loi] - 26/4/2025
Epigenetics in Development
- Epigenetic Basis for the Differentiation Potential of Mesenchymal and Embryonic Stem Cells
- Understanding the relationship between DNA methylation and histone lysine methylation
Class Exercises
- Exercise 1. Explain the Figure 2 in the paper
- Exercise 2. Explain the Figure 1 in the paper
- Exercise 3. Explain the Figure 1 in the paper
08.1 Mining Gene Expression GTEX and Epigenome Roadmap [Hung] - 26/4/2025
09.0 Epigenetics and Human Disease [Loi] - 03/5/2025
From Rett Syndrome to Epigenetic Disease
- How Mutations in the MECP2 Gene Cause Rett Syndrome
- Rett Syndrome: Genomes, Epigenomes and Neuropsychiatric
- Pathogenesis of MeCP2 Disorders
- Possible Future Therapies for Rett Syndrome
- Mouse model
Cancer Development and Metastasis
Class Exercises
- Exercise 1. Explain the Figure 1
- Exercise 2. Explain the Figure 1 to 5 in the paper
- Exercise 3. Explain the Figure 1 to 8 in the paper
- Exercise 4. Explain the Figure 1 and 2 in the paper
Home Reading
- Role of Epigenetics in Neural Differentiation:Implications for Health and Disease
- Molecular genetics of Rett syndrome: when DNA methylation goes unrecognized
09.1 Mining IHEC and TCGA database [Hung] - 03/5/2025
10.0 Epigenetic Biomarkers and Therapy [Loi] - 10/5/2025
10.1 Course Review [Loi] - 10/5/2025
10.2 Bulk RNA-seq vs DNA-seq Analysis - 10/5/2025
10.3 cBioPortal [Hung] - 10/5/2025
11. Mechanisms of epigenetic control in plant I [Nguyen] - 17/5/2025
12. Mechanisms of epigenetic control in plant II [Nguyen] - 24/5/2025